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https://www.readbyqxmd.com/read/28735484/microsphere-based-assessment-of-dna-methylation-for-aml-prognosis
#1
Gerald B W Wertheim, Marlise R Luskin, Martin Carroll, Stephen R Master
Epigenetic dysregulation, including aberrant methylation of cytosine residues in DNA, is a hallmark of cancer and clearly results in oncogenic cellular alterations such as transcriptional attenuation of tumor suppressors and genomic instability. A number of studies have examined DNA methylation alterations in patients with acute myeloid leukemia (AML) and have shown that analysis of multilocus methylation patterns can identify biologically distinct AML subclasses and can predict patient prognosis. In order to utilize the prognostic capability of methylation analysis in a clinical setting, we have developed a microsphere-based HpaII tiny fragment enrichment by ligation-mediated PCR (xMELP) assay to interrogate the methylation state of genomic multiple loci along with a random forest-based classification algorithm that correlates DNA methylation status with patient prognosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734529/ultrasound-based-differentiation-of-malignant-and-benign-thyroid-nodules-an-extreme-learning-machine-approach
#2
Jianfu Xia, Huiling Chen, Qiang Li, Minda Zhou, Limin Chen, Zhennao Cai, Yang Fang, Hong Zhou
BACKGROUND AND OBJECTIVES: It is important to be able to accurately distinguish between benign and malignant thyroid nodules in order to make appropriate clinical decisions. The purpose of this study was to improve the effectiveness and efficiency for discriminating the malignant from benign thyroid cancers based on the Ultrasonography (US) features. METHODS: There were 114 benign nodules in 106 patients (82 women and 24 men) and 89 malignant nodules in 81 patients (69 women and 12 men) included in this study...
August 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28733977/molecular-classification-of-tumor-cells-in-a-patient-with-intravascular-large-b-cell-lymphoma
#3
W M Bauer, M C Aichelburg, J Griss, C Skrabs, I Simonitsch-Klupp, A I Schiefer, H Kittler, U Jäger, M Zeyda, R Knobler, G Stingl
BACKGROUND: Intravascular large B-cell lymphoma (IVLBCL) is a rare type of extranodal large B-cell lymphoma. It is characterized by the proliferation of tumour cells exclusively intraluminally in small blood vessels of different organs. The clinical manifestation depends on the type of organ affected, additionally, a haemophagocytic syndrome can be observed in some patients. OBJECTIVE: Due to the rarity of this lymphoma and in spite of detailed immunohistochemical investigations the exact nosology of this cancer is only incompletely understood...
July 22, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28733194/breast-cancer-molecular-stratification-from-intrinsic-subtypes-to-integrative-clusters
#4
REVIEW
Hege G Russnes, Ole Christian Lingjærde, Anne-Lise Børresen-Dale, Carlos Caldas
Breast carcinomas can be stratified into different entities based on clinical behavior, histological features and/or by biological properties. A classification of breast cancer should be based on underlying biology, which we know must be determined by the somatic genomic landscape of mutations. Moreover, as the latest generations of anti-cancer agents are founded on biological mechanisms, a detailed molecular stratification is a requirement for appropriate clinical management. Such stratification, based on genomic drivers, will be important for selecting patients for clinical trials...
July 18, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28731050/genomic-abnormalities-in-invasive-endocervical-adenocarcinoma-correlate-with-pattern-of-invasion-biologic-and-clinical-implications
#5
Anjelica Hodgson, Yutaka Amemiya, Arun Seth, Matthew Cesari, Bojana Djordjevic, Carlos Parra-Herran
The pattern-based classification system for HPV-related endocervical adenocarcinoma, which classifies tumors based on the destructiveness of stromal invasion, is predictive of the risk of nodal metastases and adverse outcome. Previous studies have demonstrated clinically important molecular alterations in endocervical adenocarcinoma, including KRAS and PIK3CA mutations; however, correlation between the molecular landscape and pathological variables including pattern of invasion has not been thoroughly explored...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28730761/tumor-infiltrating-lymphocytes-as-a-prognostic-factor-in-malignant-melanoma-review-of-the-literature
#6
Vlad A Gata, Cosmin I Lisencu, Catalin I Vlad, Doina Piciu, Alexandru Irimie, Patriciu Achimas-Cadariu
Malignant melanoma represents the major cause of mortality among skin cancers, with increasing incidence and mortality rates worldwide. Despite the numerous public health campaigns and the efforts undertaken in the last decade regarding the establishment of a rapid diagnostic and an efficient treatment for these patients, the long-term prognosis has not been significantly improved. Thus, numerous studies were conducted in order to establish a more accurate prognosis, tumor infiltrating lymphocytes (TILs) being considered in many studies as independent prognostic factors of lymph node metastasis and overall survival in patients with melanoma...
May 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28730335/clinical-and-prognosis-value-of-the-cimp-status-combined-with-mlh1-or-p16-ink4a-methylation-in-colorectal-cancer
#7
Amana Saadallah-Kallel, Rania Abdelmaksoud-Dammak, Mouna Triki, Slim Charfi, Abdelmajid Khabir, Tahia Sallemi-Boudawara, Raja Mokdad-Gargouri
Aberrant DNA methylation of CpG islands occurred frequently in CRC and associated with transcriptional silencing of key genes. In this study, the CIMP combined with MLH1 or p16 (INK4a) methylation status was determined in CRC patients and correlated with clinicopathological parameters and overall survival. Our data showed that CIMP+ CRCs were identified in 32.9% of cases and that CACNAG1 is the most frequently methylated promoter. When we combined the CIMP with the MLH1 or the p16 (INK4a) methylation status, we found that CIMP-/MLH1-U (37...
August 2017: Medical Oncology
https://www.readbyqxmd.com/read/28730250/metastatic-high-grade-myxofibrosarcoma-review-of-a-clinical-case
#8
Tiberiu Paul Neagu, Ruxandra Diana Sinescu, Valentin Enache, Sanda Claudia Achim, Mirela Ţigliş, Liliana Elena Mirea
We present the particular clinical and histological features of a metastatic high-grade myxofibrosarcoma (MFS) of the left buttock in a 77-year-old male patient. The tumor was biopsied and surgically removed in order to increase the patient's comfort, due to its increased size and aggressive clinical behavior. Computed tomography (CT) revealed metastases in the pleura and mediastinal lymph nodes, so limb-sparing tumor excision followed by palliative care was the best practice for the patient until the fatal outcome...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28730229/molecular-analysis-of-brca1-and-brca2-genes-by-next-generation-sequencing-and-ultrastructural-aspects-of-breast-tumor-tissue
#9
Corina Elena Mihalcea, Ana Maria Moroşanu, Daniela Murăraşu, Liliana Puiu, Sabin Aurel Cinca, Silviu Cristian Voinea, Nicolae Mirancea
In this paper, we focus our interest on the dynamics alterations of the tumor-stroma interface at the ultrastructural level and to detect BRCA1 and BRCA2 mutations using next generation sequencing (NGS) of breast tumor tissue. Electron microscopic investigation revealed some peculiar infrastructural alterations of the tumor cells per se as well as of the tumor-stroma interface: invadopodia, shedding microvesicles, altered morphology and reduced number of telocytes, different abnormalities of the microvasculature...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28729773/is-new-american-thyroid-association-risk-classification-for-hereditary-medullary-thyroid-carcinoma-applicable-to-chinese-patients-a-single-center-study
#10
Xiwei Zhang, Dangui Yan, Junyi Wang, Hanfeng Wan, Yongxia Zhang, Yabing Zhang, Yuqin He, Wensheng Liu, Bin Zhang
OBJECTIVE: The American Thyroid Association (ATA) proposed a new risk classification for hereditary medullary thyroid carcinoma (MTC) in 2015. This study aimed to assess whether the new guidelines are suitable for the Chinese population, and reported our experience on prophylactic thyroidectomy. METHODS: A total of 73 patients from 22 families were screened as rearranged during transfection (RET) mutation carriers from 2010 to 2016 in Cancer Hospital, Chinese Academy of Medical Science; the medical history for each patient was collected...
June 2017: Chinese Journal of Cancer Research, Chung-kuo Yen Cheng Yen Chiu
https://www.readbyqxmd.com/read/28729178/elevated-cardiovascular-disease-risk-in-patients-with-chronic-myelogenous-leukemia-seen-in-community-based-oncology-practices-in-the-united-states
#11
Anna D Coutinho, Dinara Makenbaeva, Eileen Farrelly, Pamela B Landsman-Blumberg, Daniel Lenihan
INTRODUCTION: Current National Comprehensive Cancer Network guidelines recommend that comorbidities, including cardiovascular disease (CVD), be considered when selecting tyrosine kinase inhibitors for the treatment of chronic myelogenous leukemia (CML). We report here the prevalence of CVD and its risk factors in patients with CML treated by community-based United States (US) oncologists. PATIENTS AND METHODS: Adult patients with a confirmed diagnosis of CML and ≥ 1 encounter after the first date of CML diagnosis in an electronic medical record database between January 1, 2005 and October 31, 2014 were enrolled...
June 17, 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28728542/clove-classification-of-genomic-fusions-into-structural-variation-events
#12
Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T Papenfuss
BACKGROUND: A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than one breakpoint or fusion)...
July 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28728151/a-modified-classification-of-prognostic-factors-based-on-pathological-stage-and-tumor-regression-grade-in-patients-with-rectal-cancer-who-receive-preoperative-chemoradiotherapy
#13
Toshiyuki Suzuki, Sotaro Sadahiro, Akira Tanaka, Kazutake Okada, Gota Saito, Hiroshi Miyakita, Takeshi Akiba, Hiroshi Yamamuro
OBJECTIVE: The histologic response to neoadjuvant chemoradiotherapy (CRT) has been intimately related to outcomes in locally advanced rectal cancer. However, reliable prognostic factors have yet to be established. SUBJECTS AND METHODS: The study group comprised 198 patients with locally advanced rectal cancer who received CRT. A modified classification based on the combination of ypStage and tumor regression grade (TRG) was developed. ypStage II with TRG 2 was classified as ypTRGstage IIA, and ypStage II with TRG 3 or 4 was classified as ypTRGstage IIB...
July 21, 2017: Oncology
https://www.readbyqxmd.com/read/28727569/comparing-the-performance-of-linear-and-nonlinear-principal-components-in-the-context-of-high-dimensional-genomic-data-integration
#14
Shofiqul Islam, Sonia Anand, Jemila Hamid, Lehana Thabane, Joseph Beyene
Linear principal component analysis (PCA) is a widely used approach to reduce the dimension of gene or miRNA expression data sets. This method relies on the linearity assumption, which often fails to capture the patterns and relationships inherent in the data. Thus, a nonlinear approach such as kernel PCA might be optimal. We develop a copula-based simulation algorithm that takes into account the degree of dependence and nonlinearity observed in these data sets. Using this algorithm, we conduct an extensive simulation to compare the performance of linear and kernel principal component analysis methods towards data integration and death classification...
July 26, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28727556/effective-screening-and-classification-of-cervical-precancer-biopsy-imagery
#15
Jaidip Jagtap, Nishigandha Patil, Abdul K Parchur, Chayanika Pantola, Asha Agarwal, Kiran Pandey, Asima Pradhan
Microscope images of biopsy samples of cervical precancers conventionally discriminated by histopathology, the current "gold standard" for cancer detection, showed that their correlation properties are segregated into different classes. The correlation domains clearly indicate increasing cellular clustering in different grades of precancer compared to their normal counterparts. This trend indicates the probability of pixel distribution of the corresponding tissue images. Because the cell density is not uniform in the higher grades, the skewness (asymmetry of a distribution), kurtosis (sharpness of a distribution), entropy (randomness), and standard deviation are affected...
July 18, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28727297/parsel-parallel-selection-of-micro-rnas-for-survival-classification-in-cancers
#16
Debajyoti Sinha, Debarka Sengupta, Sanghamitra Bandyopadhyay
It is known that tumor micro-RNAs (miRNA) can define patient survival and treatment response. We present a framework to identify miRNAs which are predictive of cancer survival. The framework attempts to rank the miRNAs by exploring their collaborative role in gene regulation. Our approach tests a significantly large number of combinatorial cases leveraging parallel computation. We carefully avoided parametric assumptions involved in evaluations of miRNA expressions but used rigorous statistical computation to assign an importance score to a miRNA...
July 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28727286/using-cell-nuclei-features-to-detect-colon-cancer-tissue-in-hematoxylin-and-eosin-stained-slides
#17
Alex Skovsbo Jørgensen, Anders Munk Rasmussen, Niels Kristian Mäkinen Andersen, Simon Kragh Andersen, Jonas Emborg, Rasmus Røge, Lasse Riis Østergaard
Currently, diagnosis of colon cancer is based on manual examination of histopathological images by a pathologist. This can be time consuming and interpretation of the images is subject to inter- and intra-observer variability. This may be improved by introducing a computer-aided diagnosis (CAD) system for automatic detection of cancer tissue within whole slide hematoxylin and eosin (H&E) stains. Cancer disrupts the normal control mechanisms of cell proliferation and differentiation, affecting the structure and appearance of the cells...
July 20, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28727276/correlation-between-microrna-expression-clinicopathological-characteristics-and-prognosis-in-patients-with-non-small-cell-lung-cancer-a-retrospective-study
#18
Xin Wang, Yi Zhang, Xiuyi Zhi
BACKGROUND: Lung cancer prognosis is related to various factors; however, the comprehensive relationship between these factors, including microRNAs (miRNAs), and lung cancer prognosis has not been determined. Thus, the aim of this study was to identify the key factors associated with lung cancer prognosis. METHODS: We retrospectively analyzed prognosis and relevant factors in 216 non-small cell lung cancer (NSCLC) patients diagnosed from January 2008 to December 2014...
July 20, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28727228/actin-gamma-1-a-new-skin-cancer-pathogenic-gene-identified-by-the-biological-feature-based-classification
#19
Xinqian Dong, Yingsheng Han, Zhen Sun, Junlong Xu
Skin cancer is the most common form of cancer that accounting for at least 40% of cancer cases around the world. This study aimed to identify skin cancer-related biological features and predict skin cancer candidate genes by employing machine learning based on biological features of known skin cancer genes. The known skin cancer-related genes were fetched from database and encoded by the enrichment scores of gene ontology and pathways. The optimal features of the skin cancer related genes were selected with a series of feature selection methods, such as mRMR, IFS, and Random Forest algorithm...
July 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28727127/the-assessment-of-overall-survival-os-after-adjuvant-chemotherapy-for-patients-with-malignant-endometrial-cancer-in-poland
#20
Zbigniew Teter, Andrzej Śliwczyński, Melania Brzozowska, Marcin Świerkowski, Andrzej Jacyna, Jarosław Pinkas, Aleksandra Sierocka, Michał Marczak, Anna Dańska-Bidzińska, Mariusz Bidziński, Waldemar Wierzba
OBJECTIVES: In 2013 malignant endometrial cancers have amounted to 7.3% of all cancers diagnosed among women in the report by the Polish National Cancer Registry Raw prevalence rate amounted to 28.7, whereas standardised prevalence rate 15.6 per 100 000 population. Among the causes of death, these cancers amounted to 3% and were ranked ninth on the list of the most common causes of oncologic mortality of women. In the year 2013 a total of 1243 women died of malignant endometrial cancers...
2017: Ginekologia Polska
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