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Lung Genome CT

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https://www.readbyqxmd.com/read/29206898/somatic-mutation-footprinting-reveals-a-unique-tetra-nucleotide-signature-associated-with-intron-exon-boundaries-in-lung-cancer
#1
Samuel Wormald, Anita Lerch, Dmitri Mouradov, Liam O'Connor
Cigarette smoke comprises a large number of carcinogenic substances that can increase DNA mutation load in epithelial cells of the mouth, throat and lungs. While a strong C:A substitution preference is abundant in tobacco-related cancer genomes, detection of complex or less abundant somatic mutation signatures may be confounded by the heterogeneity of carcinogens present in smoke. Tri-nucleotide signatures are defined for a variety of somatic mutation processes, yet the extent to which this configuration optimally defines and discriminates between mutational processes is not clear...
December 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29168346/cancer-testis-gene-piwil1-promotes-cell-proliferation-migration-and-invasion-in-lung-adenocarcinoma
#2
Kaipeng Xie, Kai Zhang, Jing Kong, Cheng Wang, Yayun Gu, Cheng Liang, Tingting Jiang, Na Qin, Jibin Liu, Xuejiang Guo, Ran Huo, Mingxi Liu, Hongxia Ma, Juncheng Dai, Zhibin Hu
Piwi-like RNA-mediated gene silencing 1 (PIWIL1) has been identified as a novel extremely highly expressed cancer-testis (CT) gene in lung adenocarcinoma. However, the exact function and mechanism of PIWIL1 in lung adenocarcinoma remains unclear. Herein, we sought to investigate the role of PIWIL1 in the occurrence and development of lung adenocarcinoma. We examined the expression pattern of PIWIL1 in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples, and validated it by Real-Time PCR (RT-PCR) in additional 21 paired lung adenocarcinoma tissues and 16 normal tissues...
November 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/29159886/radiomics-in-lung-cancer-its-time-is-here
#3
Mannudeep Kalra, Ge Wang, Colin G Orton
Of the 8.8 million deaths from cancer in 2015, per the World Health Organization, lung cancer was the most common cause of death (1.69 million). With the introduction of low-dose CT for lung cancer screening and emergence of precision medicine for often-fatal lung cancer, there is a need for deep access to critical information, i.e. radiomics, not possible with conventional subjective interpretation of CT images. Quantitative image analyses for radiomics have been applied in lung cancers to determine their spatial complexity, genomic composition, viability or aggressiveness, and responses to targeted therapies...
November 21, 2017: Medical Physics
https://www.readbyqxmd.com/read/29149880/analytical-performance-of-envisia-a-genomic-classifier-for-usual-interstitial-pneumonia
#4
Yoonha Choi, Jiayi Lu, Zhanzhi Hu, Daniel G Pankratz, Huimin Jiang, Manqiu Cao, Cristina Marchisano, Jennifer Huiras, Grazyna Fedorowicz, Mei G Wong, Jessica R Anderson, Edward Y Tom, Joshua Babiarz, Urooj Imtiaz, Neil M Barth, P Sean Walsh, Giulia C Kennedy, Jing Huang
BACKGROUND: Clinical guidelines specify that diagnosis of interstitial pulmonary fibrosis (IPF) requires identification of usual interstitial pneumonia (UIP) pattern. While UIP can be identified by high resolution CT of the chest, the results are often inconclusive, making surgical lung biopsy necessary to reach a definitive diagnosis (Raghu et al., Am J Respir Crit Care Med 183(6):788-824, 2011). The Envisia genomic classifier differentiates UIP from non-UIP pathology in transbronchial biopsies (TBB), potentially allowing patients to avoid an invasive procedure (Brown et al...
November 17, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/29110840/immunohistochemical-and-genetic-characteristics-of-lung-cancer-mimicking-organizing-pneumonia
#5
Tomohiro Ichikawa, Koichi Saruwatari, Sachiyo Mimaki, Masato Sugano, Keiju Aokage, Motohiro Kojima, Tomoyuki Hishida, Satoshi Fujii, Junji Yoshida, Takeshi Kuwata, Atsushi Ochiai, Kenji Suzuki, Masahiro Tsuboi, Koichi Goto, Katsuya Tsuchihara, Genichiro Ishii
INTRODUCTION: Lung cancer mimicking organizing pneumonia (LCOP) is a novel radiological entity of lung adenocarcinoma that could be misdiagnosed as inflammatory lesions. However, the characteristic biological and genetic features of LCOP are not fully clarified. MATERIALS AND METHODS: We used thin-section CT images to select cases of (LCOP) among surgically resected lung adenocarcinoma patients. We compared the clinicopathological characteristics and the immunophenotypes of LCOP (n=44) and other lepidic-predominant adenocarcinomas (non-LCOP, n=56)...
November 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28972005/phenotypic-characterisation-of-eif2ak4-mutation-carriers-in-a-large-cohort-of-patients-diagnosed-clinically-with-pulmonary-arterial-hypertension
#6
Charaka Hadinnapola, Marta Bleda, Matthias Haimel, Nicholas Screaton, Andrew J Swift, Peter Dorfmüller, Stephen D Preston, Mark Southwood, Jules Hernandez-Sanchez, Jennifer Martin, Carmen Treacy, Katherine Yates, Harm Bogaard, Colin Church, Gerry Coghlan, Robin Condliffe, Paul A Corris, Simon R Gibbs, Barbara Girerd, Simon Holden, Marc Humbert, David G Kiely, Allan Lawrie, Rajiv D Machado, Robert MacKenzie Ross, Shahin Moledina, David Montani, Michael Newnham, Andrew J Peacock, Joanna Pepke-Zaba, Paula J Rayner-Matthews, Olga Shamardina, Florent Soubrier, Laura Southgate, Jay Suntharalingam, Mark R Toshner, Richard C Trembath, Anton Vonk Noordegraaf, Martin R Wilkins, Stephen J Wort, John Wharton, Stefan Gräf, Nicholas W Morrell
Background -Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease and pulmonary capillary haemangiomatosis (PVOD/PCH). Here, we determined the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH...
September 28, 2017: Circulation
https://www.readbyqxmd.com/read/28685087/heterogeneity-in-the-colorectal-primary-tumor-and-the-synchronous-resected-liver-metastases-prior-to-and-after-treatment-with-an-anti-egfr-monoclonal-antibody
#7
Daniela Adua, Francesca Di Fabio, Giorgio Ercolani, Michelangelo Fiorentino, Elisa Gruppioni, Annalisa Altimari, Fabiola Lorena Rojas Limpe, Nicola Normanno, Antonio Daniele Pinna, Carmine Pinto
Molecular heterogeneity between primary tumors (PTs) and synchronous resected liver metastasis in colorectal cancer (CRC) has potential relevance in treatment strategies. Next-generation sequencing (NGS) may be able to increase the chances of identifying multiple molecular driver alterations, calling for therapy. The aim of the present study was to evaluate mutations in PT and synchronous resected liver metastases for patients with Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) exon 2 wild-type metastatic (m)CRC who underwent chemotherapy (CT) featuring an anti-epidermal growth factor receptor (EGFR) monoclonal antibody...
July 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28521775/genome-wide-association-study-of-subclinical-interstitial-lung-disease-in-mesa
#8
Ani Manichaikul, Xin-Qun Wang, Li Sun, Josée Dupuis, Alain C Borczuk, Jennifer N Nguyen, Ganesh Raghu, Eric A Hoffman, Suna Onengut-Gumuscu, Emily A Farber, Joel D Kaufman, Dan Rabinowitz, Karen D Hinckley Stukovsky, Steven M Kawut, Gary M Hunninghake, George R Washko, George T O'Connor, Stephen S Rich, R Graham Barr, David J Lederer
BACKGROUND: We conducted a genome-wide association study (GWAS) of subclinical interstitial lung disease (ILD), defined as high attenuation areas (HAA) on CT, in the population-based Multi-Ethnic Study of Atherosclerosis Study. METHODS: We measured the percentage of high attenuation areas (HAA) in the lung fields on cardiac CT scan defined as voxels with CT attenuation values between -600 and -250 HU. Genetic analyses were performed in MESA combined across race/ethnic groups: non-Hispanic White (n = 2,434), African American (n = 2,470), Hispanic (n = 2,065) and Chinese (n = 702), as well as stratified by race/ethnicity...
May 18, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28487426/digitally-barcoding-mycobacterium-tuberculosis-reveals-in-vivo-infection-dynamics-in-the-macaque-model-of-tuberculosis
#9
Constance J Martin, Anthony M Cadena, Vivian W Leung, Philana Ling Lin, Pauline Maiello, Nathan Hicks, Michael R Chase, JoAnne L Flynn, Sarah M Fortune
Infection with Mycobacterium tuberculosis causes a spectrum of outcomes; the majority of individuals contain but do not eliminate the infection, while a small subset present with primary active tuberculosis (TB) disease. This variability in infection outcomes is recapitulated at the granuloma level within each host, such that some sites of infection can be fully cleared while others progress. Understanding the spectrum of TB outcomes requires new tools to deconstruct the mechanisms underlying differences in granuloma fate...
May 9, 2017: MBio
https://www.readbyqxmd.com/read/28464886/a-lung-cancer-risk-classifier-comprising-genome-maintenance-genes-measured-in-normal-bronchial-epithelial-cells
#10
Jiyoun Yeo, Erin L Crawford, Xiaolu Zhang, Sadik Khuder, Tian Chen, Albert Levin, Thomas M Blomquist, James C Willey
BACKGROUND: Annual low dose CT (LDCT) screening of individuals at high demographic risk reduces lung cancer mortality by more than 20%. However, subjects selected for screening based on demographic criteria typically have less than a 10% lifetime risk for lung cancer. Thus, there is need for a biomarker that better stratifies subjects for LDCT screening. Toward this goal, we previously reported a lung cancer risk test (LCRT) biomarker comprising 14 genome-maintenance (GM) pathway genes measured in normal bronchial epithelial cells (NBEC) that accurately classified cancer (CA) from non-cancer (NC) subjects...
May 2, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28422979/correlation-of-egfr-or-kras-mutation-status-with-18f-fdg-uptake-on-pet-ct-scan-in-lung-adenocarcinoma
#11
Kazuya Takamochi, Kaoru Mogushi, Hideya Kawaji, Kota Imashimizu, Mariko Fukui, Shiaki Oh, Masayoshi Itoh, Yoshihide Hayashizaki, Weijey Ko, Masao Akeboshi, Kenji Suzuki
BACKGROUND: 18F-fluoro-2-deoxy-glucose (18F-FDG) positron emission tomography (PET) is a functional imaging modality based on glucose metabolism. The correlation between EGFR or KRAS mutation status and the standardized uptake value (SUV) of 18F-FDG PET scanning has not been fully elucidated. METHODS: Correlations between EGFR or KRAS mutation status and clinicopathological factors including SUVmax were statistically analyzed in 734 surgically resected lung adenocarcinoma patients...
2017: PloS One
https://www.readbyqxmd.com/read/28285684/dual-occurrence-of-alk-g1202r-solvent-front-mutation-and-small-cell-lung-cancer-transformation-as-resistance-mechanisms-to-second-generation-alk-inhibitors-without-prior-exposure-to-crizotinib-pitfall-of-solely-relying-on-liquid-re-biopsy
#12
Sai-Hong Ignatius Ou, Thomas K Lee, Lauren Young, Maria Y Fernandez-Rocha, Dean Pavlick, Alexa B Schrock, Viola W Zhu, Jeffrey Milliken, Siraj M Ali, Barbara J Gitlitz
Development of the acquired ALK G1202R solvent front mutation and small cell lung cancer (SCLC) transformation have both been independently reported as resistance mechanisms to ALK inhibitors in ALK-rearranged (ALK+) non-small cell lung cancer (NSCLC) patients but have not been reported in the same patient. Here we report an ALK+ NSCLC patient who had disease progression after ceritinib and then alectinib where an ALK G1202R mutation was detected on circulating tumor (ct) DNA prior to enrollment onto a trial of another next generation ALK inhibitor, lorlatinib...
April 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28139704/predictive-radiogenomics-modeling-of-egfr-mutation-status-in-lung-cancer
#13
Olivier Gevaert, Sebastian Echegaray, Amanda Khuong, Chuong D Hoang, Joseph B Shrager, Kirstin C Jensen, Gerald J Berry, H Henry Guo, Charles Lau, Sylvia K Plevritis, Daniel L Rubin, Sandy Napel, Ann N Leung
Molecular analysis of the mutation status for EGFR and KRAS are now routine in the management of non-small cell lung cancer. Radiogenomics, the linking of medical images with the genomic properties of human tumors, provides exciting opportunities for non-invasive diagnostics and prognostics. We investigated whether EGFR and KRAS mutation status can be predicted using imaging data. To accomplish this, we studied 186 cases of NSCLC with preoperative thin-slice CT scans. A thoracic radiologist annotated 89 semantic image features of each patient's tumor...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074712/high-throughput-whole-genome-sequencing-of-porcine-reproductive-and-respiratory-syndrome-virus-from-cell-culture-materials-and-clinical-specimens-using-next-generation-sequencing-technology
#14
Jianqiang Zhang, Ying Zheng, Xiao-Qin Xia, Qi Chen, Sarah A Bade, Kyoung-Jin Yoon, Karen M Harmon, Phillip C Gauger, Rodger G Main, Ganwu Li
Next-generation sequencing (NGS) technologies have increasingly played crucial roles in biological and medical research, but are not yet in routine use in veterinary diagnostic laboratories. We developed and applied a procedure for high-throughput RNA sequencing of Porcine reproductive and respiratory syndrome virus (PRRSV) from cell culture-derived isolates and clinical specimens. Ten PRRSV isolates with known sequence information, 2 mixtures each with 2 different PRRSV isolates, and 51 clinical specimens (19 sera, 16 lungs, and 16 oral fluids) with various PCR threshold cycle (Ct) values were subjected to nucleic acid extraction, cDNA library preparation (24-plexed), and sequencing...
January 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28009417/multiple-chromophobe-and-clear-cell-renal-cancer-in-a-patient-affected-by-birt-hogg-dub%C3%A3-syndrome-a-case-report
#15
Roberto Castellucci, Michele Marchioni, Sergio Valenti, Giusepe Sortino, Giulio Borgonovo, Nicola Pesenti, Alberto C A Vismara, Maria C Circo, Barbara Sessa, Emanuele Micheli, Antonino Lembo
OBJECTIVES: Birt-Hogg-Dubé syndrome (BHDS) is a rare autosomal dominant characterized by the presence of fibrofolliculomas and/or trichodiscomas, pulmonary cysts, spontaneous pneumothorax, and renal tumors. The syndrome is linked to mutations in the FLCN gene, which is preferentially expressed in the skin, kidney, and lung. The aim of our paper is to describe a case of multiple bilateral renal cancer in a patient affected by BHDS. CASE PRESENTATION: Patient subjected to enucleoresection seven kidney tumors discovered right after ultrasound performed for other reasons...
December 16, 2016: Urologia
https://www.readbyqxmd.com/read/27932290/the-diagnosis-of-idiopathic-pulmonary-fibrosis-current-and-future-approaches
#16
REVIEW
Fernando J Martinez, Alison Chisholm, Harold R Collard, Kevin R Flaherty, Jeffrey Myers, Ganesh Raghu, Simon L F Walsh, Eric S White, Luca Richeldi
With the recent development of two effective treatments for patients with idiopathic pulmonary fibrosis, an accurate diagnosis is crucial. The traditional approach to diagnosis emphasises the importance of thorough clinical and laboratory evaluations to exclude secondary causes of disease. High-resolution CT is a critical initial diagnostic test and acts as a tool to identify patients who should undergo surgical lung biopsy to secure a definitive histological diagnosis of usual interstitial pneumonia pattern...
January 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/27871249/benign-clear-cell-sugar-tumor-of-the-lung-in-a-patient-with-birt-hogg-dub%C3%A3-syndrome-a-case-report
#17
Yoko Gunji-Niitsu, Toshio Kumasaka, Shigehiro Kitamura, Yoshito Hoshika, Takuo Hayashi, Hitoshi Tokuda, Riichiro Morita, Etsuko Kobayashi, Keiko Mitani, Mika Kikkawa, Kazuhisa Takahashi, Kuniaki Seyama
BACKGROUND: Birt-Hogg-Dubé (BHD) syndrome is a rare inherited autosomal genodermatosis and caused by germline mutation of the folliculin (FLCN) gene, a tumor suppressor gene of which protein product is involved in mechanistic target of rapamycin (mTOR) signaling pathway regulating cell growth and metabolism. Clinical manifestations in BHD syndrome is characterized by fibrofolliculomas of the skin, pulmonary cysts with or without spontaneous pneumothorax, and renal neoplasms. There has been no pulmonary neoplasm reported in BHD syndrome, although the condition is due to deleterious sequence variants in a tumor suppressor gene...
November 21, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27856720/nondestructive-cryomicro-ct-imaging-enables-structural-and-molecular-analysis-of-human-lung-tissue
#18
Dragoş M Vasilescu, André B Phillion, Naoya Tanabe, Daisuke Kinose, David F Paige, Jacob J Kantrowitz, Gang Liu, Hanqiao Liu, Nick Fishbane, Stijn E Verleden, Bart M Vanaudenaerde, Marc Lenburg, Christopher S Stevenson, Avrum Spira, Joel D Cooper, Tillie-Louise Hackett, James C Hogg
Micro-computed tomography (CT) enables three-dimensional (3D) imaging of complex soft tissue structures, but current protocols used to achieve this goal preclude cellular and molecular phenotyping of the tissue. Here we describe a radiolucent cryostage that permits micro-CT imaging of unfixed frozen human lung samples at an isotropic voxel size of (11 µm)(3) under conditions where the sample is maintained frozen at -30°C during imaging. The cryostage was tested for thermal stability to maintain samples frozen up to 8 h...
January 1, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/27794398/case-report-durable-response-to-afatinib-in-a-patient-with-lung-cancer-harboring-two-uncommon-mutations-of-egfr-and-a-kras-mutation
#19
Junko Tanizaki, Eri Banno, Yosuke Togashi, Hidetoshi Hayashi, Kazuko Sakai, Masayuki Takeda, Hiroyasu Kaneda, Kazuto Nishio, Kazuhiko Nakagawa
Comprehensive genomic profiling for non-small cell lung cancer (NSCLC) is likely to identify more patients with rare genetic alterations including uncommon epidermal growth factor receptor gene (EGFR) mutations. It remains unclear how such patients should be treated, however. We here report a case of NSCLC positive for two uncommon mutations of EGFR and a KRAS mutation, including its treatment with the second-generation EGFR tyrosine kinase inhibitor (TKI) afatinib. Tumor specimen obtained by a NSCLC patient with no smoking history was analyzed by next-generation sequencing...
November 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/27755912/genomic-adequacy-from-solid-tumor-core-needle-biopsies-of-ex-vivo-tissue-and-in-vivo-lung-masses-prospective-study
#20
Neema Jamshidi, Danshan Huang, Fereidoun G Abtin, Christopher T Loh, Stephen T Kee, Robert D Suh, Shota Yamamoto, Kingshuk Das, Sarah Dry, Scott Binder, Dieter R Enzmann, Michael D Kuo
Purpose To identify the variables and factors that affect the quantity and quality of nucleic acid yields from imaging-guided core needle biopsy. Materials and Methods This study was approved by the institutional review board and compliant with HIPAA. The authors prospectively obtained 232 biopsy specimens from 74 patients (177 ex vivo biopsy samples from surgically resected masses were obtained from 49 patients and 55 in vivo lung biopsy samples from computed tomographic [CT]-guided lung biopsies were obtained from 25 patients) and quantitatively measured DNA and RNA yields with respect to needle gauge, number of needle passes, and percentage of the needle core...
March 2017: Radiology
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