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molecular subtyping

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https://www.readbyqxmd.com/read/30425968/high-sensitive-and-non-invasive-ctdnas-sequencing-facilitate-clinical-diagnosis-and-clinical-guidance-of-non-small-cell-lung-cancer-patient-a-time-course-study
#1
Yongqiang Li, Jiajia Lv, Shaogui Wan, Junfang Xin, Tiantian Xie, Tao Li, Wan Zhu, Guosen Zhang, Yunlong Wang, Yitai Tang, Ao Li, Xiangqian Guo
Lung cancer is one of leading causes of cancer death all over the world. Non-small cell lung cancer (NSCLC) is the most predominant subtype of lung cancer. Molecular targeting therapy has been shown great success in the treatment of advanced NSCLC. Thus, an easy, sensitive, and specific way of recognizing therapeutic gene targets would help to select effective treatments, to improve physical condition and increase patient survival. In this study, we recruited and followed up a female NSCLC patient, whose plasma ctDNAs (circulating tumor DNAs), blood cell DNAs, psDNAs (pleural effusion supernatant DNAs), and ppDNAs (pleural effusion pellet DNAs), were collected and analyzed over periodic time points by methods of next generation sequencing (NGS), droplet digital PCR (ddPCR), and Amplification Refractory Mutation System (ARMS)...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/30425937/lymphocyte-subsets-predictive-value-and-possible-involvement-of-human-papilloma-virus-infection-on-breast-cancer-molecular-subtypes
#2
Andreína Fernandes, Adriana Pesci-Feltri, Isabel García-Fleury, Marco López, Vincent Guida, Marisol De Macedo, María Correnti
AIM: To detect human papilloma virus (HPV) presence and to characterize cellular immune response in breast cancer patients. METHODS: A total of 74 women were included, of which 48 samples were from patients diagnosed with breast cancer and 26 patients with benign pathology of the breast. Molecular subtype classification was performed based on the immunohistochemical reports of the tumor piece. HPV genome detection and genotyping from fresh breast biopsies was performed using the INNO-LIPA HPV Genotyping Extra test (Innogenetics, Ghent, Belgium)...
November 10, 2018: World Journal of Clinical Oncology
https://www.readbyqxmd.com/read/30425522/clinical-characterization-of-erbb2-exon-20-insertions-and-heterogeneity-of-outcomes-responding-to-afatinib-in-chinese-lung-cancer-patients
#3
Zhefeng Liu, Lin Wu, Jun Cao, Zhe Yang, Chengzhi Zhou, Liming Cao, Hao Wu, Haibo Shen, Meiling Jin, Yong Zhang, Xinru Mao, Jianxing Xiang, Ke Ma, Bing Li, Tengfei Zhang, Yi Hu
Purpose: ERBB2 exon 20 insertions (20ins) have been identified as oncogenic drivers in lung cancers. Lung cancer patients with 20ins benefit from afatinib. However, response heterogeneity was observed in patients harboring different 20ins subtypes. In this study, we interrogated clinical characteristics in ERBB2 -mutated Chinese lung cancer and investigated the clinical outcomes of specific ERBB2 20ins in response to afatinib. Experimental design: In this study, we retrospectively collected genomic profiling data of 7,520 lung cancer patients sequenced using next-generation sequencing in a Clinical Laboratory Improvement Amendments-certified laboratory...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/30425335/rhoa-mutations-and-cldn18-arhgap-fusions-in-intestinal-type-adenocarcinoma-with-anastomosing-glands-of-the-stomach
#4
Taiki Hashimoto, Reiko Ogawa, Tzu-Yin Tang, Hiroshi Yoshida, Hirokazu Taniguchi, Hitoshi Katai, Ichiro Oda, Shigeki Sekine
A subtype of intestinal-type adenocarcinoma of the stomach, characterized by low-grade cytological atypia and anastomosing glands, has been described in several reports under different names. One of the remarkable features of these lesions, herein referred to as intestinal-type adenocarcinoma with anastomosing glands, is the frequent association of poorly differentiated adenocarcinoma components. Here we analyzed 44 intestinal-type adenocarcinomas with anastomosing glands focusing on the molecular abnormalities that are common in diffuse-type gastric cancers...
November 13, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/30425251/author-correction-integrated-molecular-subtyping-defines-a-curable-oligometastatic-state-in-colorectal-liver-metastasis
#5
Sean P Pitroda, Nikolai N Khodarev, Lei Huang, Abhineet Uppal, Sean C Wightman, Sabha Ganai, Nora Joseph, Jason Pitt, Miguel Brown, Martin Forde, Kathy Mangold, Lai Xue, Christopher Weber, Jeremy P Segal, Sabah Kadri, Melinda E Stack, Sajid Khan, Philip Paty, Karen Kaul, Jorge Andrade, Kevin P White, Mark Talamonti, Mitchell C Posner, Samuel Hellman, Ralph R Weichselbaum
In the originally published version of this Article, the affiliation details for Kevin P. White inadvertently omitted 'Tempus Labs, Chicago, IL, 60654, USA'. This has now been corrected in both the PDF and HTML versions of the Article.
November 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/30423292/accurate-and-reproducible-diagnosis-of-canine-soft-tissue-sarcoma-using-mass-spectrometry-a-step-in-the-right-direction
#6
Emily Z Keung, Christina L Roland
In this issue of Cancer Cell, Saudemont et al. describe the real-time ex vivo molecular diagnosis and histologic subtyping of canine soft tissue sarcomas using SpiderMass, a technology using water-assisted laser desorption/ionization mass spectrometry. In the future, SpiderMass has the potential to aid in diagnosis and intraoperative margin assessment.
November 12, 2018: Cancer Cell
https://www.readbyqxmd.com/read/30423196/loss-of-atrx-daxx-expression-and-alternative-lengthening-of-telomeres-in-uterine-leiomyomas
#7
Terhi V Ahvenainen, Netta M Mäkinen, Pernilla von Nandelstadh, Maija E A Vahteristo, Annukka M Pasanen, Ralf C Bützow, Pia M Vahteristo
BACKGROUND: Uterine leiomyomas (ULs) are the most common gynecologic tumors and affect 3 of every 4 women by the age of 50 years. The majority of ULs are classified as conventional tumors, whereas 10% represent various histopathological subtypes with features that mimic malignancy. These subtypes include cellular and mitotically active ULs and ULs with bizarre nuclei. Uterine leiomyosarcoma (ULMS), the malignant counterpart of UL, is an aggressive cancer with poor overall survival. The early diagnosis and preoperative differentiation of ULMS from UL are often challenging because their symptoms and morphology resemble one another...
November 13, 2018: Cancer
https://www.readbyqxmd.com/read/30419615/distribution-of-hepatitis-c-virus-genotypes-and-subtypes-in-croatia-2008-2015
#8
Adriana Vince, Snježana Židovec Lepej, Jasna Bingulac-Popović, Manuela Miletić, Sendi Kuret, Sanda Sardelić, Ivana Baća Vrakela, Ivan Kurelac
OBJECTIVE: Hepatitis C virus (HCV) genotyping is an important part of pre-treatment diagnostic algorithms as it guides the choice of therapeutic regimens. The aim of this study was to analyse the distribution of HCV genotypes in patients with chronic hepatitis C from Croatia in the period 2008-2015. METHODS: The study enrolled 3,655 anti-HCV positive patients with available results of HCV genotyping from the three largest national HCV genotyping laboratories. RESULTS: The majority of HCV-infected individuals enrolled in the study were male (70...
September 2018: Central European Journal of Public Health
https://www.readbyqxmd.com/read/30419345/recent-advances-in-the-research-of-immunotherapy-for-triple-negative-breast-cancer
#9
Xiangyu Wang, Yihang Qi, Xiangyi Kong, Jie Zhai, Yalun Li, Yan Song, Jing Wang, Xiaoli Feng, Yi Fang
Triple-negative breast cancer (TNBC) refers to cancers that are low in expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). TNBC tends to behave more aggressively than other types of breast cancer. Unlike other breast cancer subtypes (ie, ER-positive, HER2-positive subtypes), there are no approved targeted treatments available, other than the administration of chemotherapy. Immunotherapy is a new kind of treatment approach for TNBC when compared with the surgical treatment, chemotherapy, endocrine therapy, and molecular targeting therapy...
November 9, 2018: Cancer Letters
https://www.readbyqxmd.com/read/30418108/molecular-characterization-of-staphylococcus-argenteus-in-myanmar-identification-of-novel-genotypes-clusters-in-staphylocoagulase-protein-a-alpha-haemolysin-and-other-virulence-factors
#10
Meiji Soe Aung, Thida San, Nilar San, Win Mar Oo, Phyoe May Ko, Khin Thet Thet, Noriko Urushibara, Mitsuyo Kawaguchiya, Ayako Sumi, Nobumichi Kobayashi
PURPOSE: Staphylococcus argenteus is a novel emerging species of coagulase-positive staphylococcus that is genetically closely related to Staphylococcus aureus. To elucidate the molecular differences in the virulence factors (staphylocoagulase, protein A, alpha-haemolysin, enterotoxin-like toxin and staphylokinase) between these staphylococcal species, S. argenteus that had recently been isolated in Myanmar (five nasal isolates and four clinical isolates) were analysed. METHODOLOGY: The nucleotide sequences of the virulence factors were determined by PCR and direct sequencing, followed by phylogenetic analysis by mega6 and multiple alignment by clustalw using the published sequence data for S...
November 12, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/30418085/systems-biology-and-machine-learning-in-plant-pathogen-interactions
#11
Bharat Mishra, Nilesh Kumar, M Shahid Mukhtar
Systems biology is an inclusive approach to study the static and dynamic emergent properties on a global scale by integrating multiomics datasets to establish qualitative and quantitative associations among multiple biological components. With an abundance of improved high throughput -omics datasets, network-based analyses and machine learning technologies are playing a pivotal role in comprehensive understanding of biological systems. Network topological features reveal most important nodes within a network as well as prioritize significant molecular components for diverse biological networks, including coexpression, protein-protein interaction, and gene regulatory networks...
November 12, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/30418040/pediatric-ependymoma-current-treatment-and-newer-therapeutic-insights
#12
Soumen Khatua, Ross Magnum, Kelsey C Bertrand, Wafik Zaky, David McCall, Stephen C Mack
Advances in genomic, transcriptomic and epigenomic profiling now identifies pediatric ependymoma as a defined biological entity. Molecular interrogation has segregated these tumors into distinct biological subtypes based on anatomical location, age and clinical outcome, which now defines the need to tailor therapy even for histologically similar tumors. These findings now provide reasons for a paradigm shift in therapy, which should profile future clinical trials focused on targeted therapeutic strategies and risk-based treatment...
November 12, 2018: Future Oncology
https://www.readbyqxmd.com/read/30417466/alternative-rna-splicing-of-the-git1-gene-is-associated-with-neuroendocrine-prostate-cancer
#13
Ahn R Lee, Yu Gan, Ning Xie, Varune R Ramnarine, Jessica M Lovnicki, Xuesen Dong
Potent androgen receptor pathway inhibition (ARPI) therapies has given rise to a lethal, aggressive subtype of castration-resistant prostate cancer (CRPC) called treatment-induced neuroendocrine prostate cancer (t-NEPC). Now, t-NEPC poses a major clinical issue as ~20% of CRPC cases bear this subtype-a rate of occurrence that is predicted to rise with the widespread use of ARPI therapies. Unfortunately, there are no targeted therapies currently available to treat t-NEPC, as the origin and molecular underpinnings of t-NEPC development remain unclear...
November 12, 2018: Cancer Science
https://www.readbyqxmd.com/read/30417146/immune-and-genomic-signatures-in-oral-head-and-neck-cancer
#14
REVIEW
Prasenjit Chakraborty, Tanusri Karmakar, Neeraj Arora, Geetashree Mukherjee
Head and neck squamous cell carcinoma (HNSCC) is responsible for a large number of deaths each year. Oral cancer is the most frequent subtype of HNSCC. Historically, oral cancer has been associated with an increase in the consumption of tobacco and alcohol products, seen especially in the Asian subcontinent. It has also been associated with infection by the human papilloma virus (HPV), particularly strain HPV16. Treatment usually involves a multidisciplinary approach of surgery combined with chemotherapy and radiation...
October 2018: Heliyon
https://www.readbyqxmd.com/read/30417054/immunology-immunotherapy-and-translating-basic-science-into-the-clinic-for-bladder-cancer
#15
Molly A Ingersoll, Xue Li, Brant A Inman, John W Greiner, Peter C Black, Rosalyn M Adam
The Fourth Annual Albert Institute Bladder Cancer Care and Research Symposium was held from September 14th-16th in Houston, Texas. The symposium covered a range of topics relevant to bladder cancer, including basic science aspects of immunology and immunotherapy that inform clinical management; intravesical therapy for non-muscle invasive disease; understanding the nuances of carcinoma in situ ; and optimizing patient care and outcomes following therapy. The moving landscape of bladder cancer from an industry perspective was also discussed...
October 29, 2018: Bladder Cancer
https://www.readbyqxmd.com/read/30416860/immunotherapy-strategy-of-egfr-mutant-lung-cancer
#16
Shaorong Yu, Delin Liu, Bo Shen, Meiqi Shi, Jifeng Feng
EGFR-mutant lung cancer is an important molecular subtype in Asia considering that almost 40%-50% of patients with lung adenocarcinoma in Asian carry the active EGFR mutaiton. People have greatly anticipated the efficacy of PD-1/PD-L1 monoclonal antibody in lung cancer treatment but anti-PD-1/PD-L1 treatment failed to positively affect these patients. The NCCN guidelines do not recommend immunotherapy to patients with NSCLC carrying EGFR mutation at present. However, the reason why EGFR-mutant lung cancer patients show poor response to anti-PD-1/PD-L1 treatment is still unknown...
2018: American Journal of Cancer Research
https://www.readbyqxmd.com/read/30416687/brain-metastases-in-alk-positive-nsclc-time-to-adjust-current-treatment-algorithms
#17
REVIEW
Frank Griesinger, Julia Roeper, Christoph Pöttgen, Kay C Willborn, Wilfried E E Eberhardt
The progress in molecular biology has revolutionized systemic treatment of advanced non-small-cell lung cancer (NSCLC) from conventional chemotherapy to a treatment stratified by histology and genetic aberrations. Tumors harboring a translocation of the anaplastic-lymphoma-kinase (ALK) gene constitute a distinct genetic and clinico-pathologic NSCLC subtype with patients with ALK-positive disease being at a higher risk for developing brain metastases. Due to the introduction of effective targeted therapy with ALK-inhibitors, today, patients with advanced ALK-positive NSCLC achieve high overall response rates and remain progression-free for long time intervals...
October 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/30415991/analysis-of-mutational-signatures-in-primary-and-metastatic-endometrial-cancer-reveals-distinct-patterns-of-dna-repair-defects-and-shifts-during-tumor-progression
#18
Charles W Ashley, Arnaud Da Cruz Paula, Rahul Kumar, Diana Mandelker, Xin Pei, Nadeem Riaz, Jorge S Reis-Filho, Britta Weigelt
OBJECTIVE: Mutational signatures provide insights into the biological processes shaping tumor genomes and may inform patient therapy. We sought to define the mutational signatures of i) endometrioid and serous endometrial carcinomas (ECs), stratified into the four molecular subtypes, ii) uterine carcinosarcomas, and iii) matched primary and metastatic ECs. METHODS: Whole-exome sequencing MC3 data from primary endometrioid and serous carcinomas (n = 232) and uterine carcinosarcomas (n = 57) from The Cancer Genome Atlas (TCGA), and matched primary and metastatic ECs (n = 61, 26 patients) were reanalyzed, subjected to mutational signature analysis using deconstructSigs, and correlated with clinicopathologic and genomic data...
November 8, 2018: Gynecologic Oncology
https://www.readbyqxmd.com/read/30412224/colorectal-premalignancy-is-associated-with-consensus-molecular-subtypes-1-and-2
#19
K Chang, J A Willis, J Reumers, M W Taggart, F A San Lucas, S Thirumurthi, P Kanth, D A Delker, C H Hagedorn, P M Lynch, L M Ellis, E T Hawk, P A Scheet, S Kopetz, J Arts, J Guinney, R Dienstmann, E Vilar
Background: Gene expression-based profiling of colorectal cancer (CRC) can be used to identify four molecularly homogeneous consensus molecular subtype (CMS) groups with unique biologic features. However, its applicability to colorectal premalignant lesions remains unknown. Patients and methods: We assembled the largest transcriptomic premalignancy dataset by integrating different public and proprietary cohorts of adenomatous and serrated polyps from sporadic (N = 311) and hereditary (N = 78) patient populations and carried out a comprehensive analysis of carcinogenesis pathways using the CMS random forest (RF) classifier...
October 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/30412075/correlation-of-tumor-uptake-on-breast-specific-gamma-imaging-and-fluorodeoxyglucose-pet-ct-with-molecular-subtypes-of-breast-cancer
#20
Soo Jin Lee, Min Sung Chung, Su-Jin Shin, Yun Young Choi
Mechanisms of technetium-99m sesta-methoxyisobutylisonitrile (sestamibi) and F-fluorodeoxyglucose (FDG) uptake by tumor are different. The purpose of this study was to investigate the association between the tumor uptake of these 2 tracers in invasive ductal carcinoma and to examine thecorrelation of uptake of each tracer with prognostic factors and tumor molecular subtypes.A total of 96 patients with invasive ductal carcinoma who underwent preoperative breast-specific gamma imaging and FDG positron-emission tomography/computed tomography were retrospectively enrolled...
October 2018: Medicine (Baltimore)
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