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https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#1
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341024/advanced-contrast-agents-for-multimodal-biomedical-imaging-based-on-nanotechnology
#2
Daniel Calle, Paloma Ballesteros, Sebastián Cerdán
Clinical imaging modalities have reached a prominent role in medical diagnosis and patient management in the last decades. Different image methodologies as Positron Emission Tomography, Single Photon Emission Tomography, X-Rays, or Magnetic Resonance Imaging are in continuous evolution to satisfy the increasing demands of current medical diagnosis. Progress in these methodologies has been favored by the parallel development of increasingly more powerful contrast agents. These are molecules that enhance the intrinsic contrast of the images in the tissues where they accumulate, revealing noninvasively the presence of characteristic molecular targets or differential physiopathological microenvironments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340409/dynamics-of-3d-carcinoma-cell-invasion-into-aligned-collagen
#3
Arja Ray, Rachel K Morford, Nima Ghaderi, David J Odde, Paolo P Provenzano
Carcinoma cells frequently expand and invade from a confined lesion, or multicellular clusters, into and through the stroma on the path to metastasis, often with an efficiency dictated by the architecture and composition of the microenvironment. Specifically, in desmoplastic carcinomas such as those of the breast, aligned collagen tracks provide contact guidance cues for directed cancer cell invasion. Yet, the evolving dynamics of this process of invasion remains poorly understood, in part due to difficulties in continuously capturing both spatial and temporal heterogeneity and progression to invasion in experimental systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29334842/a-comprehensive-review-of-endoscopic-ultrasound-core-biopsy-needles
#4
Theodore W James, Todd H Baron
Endoscopic ultrasound (EUS)-guided tissue acquisition by-fine needle biopsy (EUS-FNB) developed over the last two decades as an attempt to overcome the limitations of fine needle aspiration (FNA). There are now three commercially available second-generation FNB needles with different tip designs. Areas covered: In this review the roles of EUS-FNA and FNB, the history and evolution of the EUS core biopsy needle are addressed followed by a presentation of currently available needles. Literature search was conducted using MEDLINE, Controlled Trials Register, US Patent Registry, Google Scholar, and Conference Abstracts...
January 16, 2018: Expert Review of Medical Devices
https://www.readbyqxmd.com/read/29334678/genome-evolution-analysis-of-recurrent-testicular-malignant-mesothelioma-by-whole-genome-sequencing
#5
Shigeng Zhang, Qi Zhang, Qing Sun, Jinlong Tang, Jimin Chen, Na Ji, Yichun Zheng, Francia Fang, Wanjun Lei, Pengpeng Li, Nan Zhang
BACKGROUND/AIMS: Malignant mesothelioma of the tunica vaginalis testis is a rare and lethal disease. The genomic characteristics and genetic changes of tumor cells during the progression of this disease are unknown. METHODS: we performed whole-genome sequencing of four successive tumor samples derived from surgery and a blood sample in a single patient. RESULTS: All tumors were found to have significant C-to-T and T-to-C mutations, and amplification of copy number in chromosomes 1 and 12 were notified in all tumor samples...
January 15, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29333831/-mammary-hemangioma-in-an-infant-with-apparent-mastitis-case-report
#6
Cristina Rodríguez Jiménez, Concepción Míguez Navarro, Minia Campos Domínguez, Carmen Garrido Colino
Mammary pathology is infrequent during childhood. It is rare the probability of finding a breast mass in an infant. The most frequent possible diagnoses at this age are breast abscess, mastitis, breast engorgement due to maternal hormonal stimulation and hemangioma. Reaching the proper diagnosis is essential in order to apply a suitable treatment and avoid the potential disease complications. We present the case of a female infant having a mass in the right breast from birth. Initially the entity was treated as mastitis...
February 1, 2018: Archivos Argentinos de Pediatría
https://www.readbyqxmd.com/read/29332326/carcinogenic-potential-of-antitumor-therapies-is-the-risk-predictable
#7
Ivanka Nenova, Janet Grudeva-Popova
The growing number of successfully cured cancer patients has created a new field in oncogenesis. The life expectancy of such patients has increased, however this favorable event may create enough time for epigenetic events to occur which can cause a new carcinognic event, i.e. a secondary malignancy. The terms in use are second primary malignancies as well as therapy-related neoplasms in case the treatment of the first neoplasm is a direct cause. Second primary malignancies can be hematological neoplasms or solid tumors, with solid tumors having higher frequency...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29331888/a-longitudinal-analysis-of-ido-and-pdl1-expression-during-immune-or-targeted-therapy-in-advanced-melanoma
#8
Lukas Krähenbühl, Simone M Goldinger, Joanna Mangana, Katrin Kerl, Ines Chevolet, Liève Brochez, Christine Horak, Mitch Levesque, Reinhard Dummer, Phil F Cheng
A deepened understanding of the cellular and molecular processes in the tumor microenvironment is necessary for the development of precision immunotherapy (IT). We simultaneously investigated CD3, PDL1, and IDO by immunohistochemistry in paired biopsies from various organs of 43 metastatic melanoma patients treated with IT and targeted therapy (TT). Intraindividual biopsies taken after a period of weeks to months demonstrate discordant results in 30% of the cases. Overlap of IDO and PDL1 increased after therapy...
January 11, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29331175/tracerx-tracking-tumor-evolution-to-impact-the-course-of-lung-cancer
#9
EDITORIAL
Marcelo Vailati Negrao, Kelly Quek, Jianjun Zhang, Boris Sepesi
No abstract text is available yet for this article.
November 16, 2017: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#10
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29324546/applying-precision-medicine-to-ovarian-cancer-proof-of-principle-for-a-molecular-second-look
#11
Melissa Schwartz, Olga Camacho-Vanegas, Ashley M Wood, Matthew Dashkoff, Courtney Whitelock, Timothy T Harkins, Carmel J Cohen, Ann Marie Beddoe, Peter Dottino, John A Martignetti
OBJECTIVES: The objectives of this study were to assess if targeted investigation for tumor-specific mutations by ultradeep DNA sequencing of peritoneal washes of ovarian cancer patients after primary surgical debulking and chemotherapy, and clinically diagnosed as disease free, provides a more sensitive and specific method to assess actual treatment response and tailor future therapy and to compare this "molecular second look" with conventional cytology and histopathology-based findings...
January 10, 2018: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29323486/a-ph-sensing-optode-for-mapping-spatiotemporal-gradients-in-3d-paper-based-cell-cultures
#12
Rachael M Kenney, Matthew W Boyce, Nathan Whitman, Brenden P Kromhout, Matthew R Lockett
Paper-based cultures are an emerging platform for preparing 3D tissue-like structures. Chemical gradients can be imposed upon these cultures, generating microenvironments similar to those found in poorly vascularized tumors. There is increasing evidence that the tumor microenvironment is responsible for promoting drug resistance and increased invasiveness. Acidosis, or the acidification of the extracellular space, is particularly important in promoting these aggressive cancer phenotypes. To better understand how cells respond to acidosis there is a need for 3D culture platforms that not only model relevant disease states, but also contain sensors capable of quantifying the extracellular environment...
January 11, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29320780/the-evolution-of-neuroendocrine-tumor-treatment-reflected-by-enets-guidelines
#13
Wouter T Zandee, Wouter W de Herder
No abstract text is available yet for this article.
January 10, 2018: Neuroendocrinology
https://www.readbyqxmd.com/read/29317634/punctuated-evolution-of-canonical-genomic-aberrations-in-uveal-melanoma
#14
Matthew G Field, Michael A Durante, Hima Anbunathan, Louis Z Cai, Christina L Decatur, Anne M Bowcock, Stefan Kurtenbach, J William Harbour
Cancer is thought to arise through the accumulation of genomic aberrations evolving under Darwinian selection. However, it remains unclear when the aberrations associated with metastasis emerge during tumor evolution. Uveal melanoma (UM) is the most common primary eye cancer and frequently leads to metastatic death, which is strongly linked to BAP1 mutations. Accordingly, UM is ideally suited for studying the clonal evolution of metastatic competence. Here we analyze sequencing data from 151 primary UM samples using a customized bioinformatic pipeline, to improve detection of BAP1 mutations and infer the clonal relationships among genomic aberrations...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29316705/translocation-breakpoints-preferentially-occur-in-euchromatin-and-acrocentric-chromosomes
#15
Cheng-Yu Lin, Ankit Shukla, John P Grady, J Lynn Fink, Eloise Dray, Pascal H G Duijf
Chromosomal translocations drive the development of many hematological and some solid cancers. Several factors have been identified to explain the non-random occurrence of translocation breakpoints in the genome. These include chromatin density, gene density and CCCTC-binding factor (CTCF)/cohesin binding site density. However, such factors are at least partially interdependent. Using 13,844 and 1563 karyotypes from human blood and solid cancers, respectively, our multiple regression analysis only identified chromatin density as the primary statistically significant predictor...
January 8, 2018: Cancers
https://www.readbyqxmd.com/read/29316430/tumor-evolution-of-glioma-intrinsic-gene-expression-subtypes-associates-with-immunological-changes-in-the-microenvironment
#16
Qianghu Wang, Baoli Hu, Xin Hu, Hoon Kim, Massimo Squatrito, Lisa Scarpace, Ana C deCarvalho, Sali Lyu, Pengping Li, Yan Li, Floris Barthel, Hee Jin Cho, Yu-Hsi Lin, Nikunj Satani, Emmanuel Martinez-Ledesma, Siyuan Zheng, Edward Chang, Charles-Etienne Gabriel Sauvé, Adriana Olar, Zheng D Lan, Gaetano Finocchiaro, Joanna J Phillips, Mitchel S Berger, Konrad R Gabrusiewicz, Guocan Wang, Eskil Eskilsson, Jian Hu, Tom Mikkelsen, Ronald A DePinho, Florian Muller, Amy B Heimberger, Erik P Sulman, Do-Hyun Nam, Roel G W Verhaak
No abstract text is available yet for this article.
January 8, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29312715/multidisciplinary-approach-to-chest-wall-resection-and-reconstruction-for-chest-wall-tumors-a-single-center-experience
#17
Elisa Scarnecchia, Valeria Liparulo, Alessandra Pica, Giuseppe Guarro, Carmine Alfano, Francesco Puma
Background: Chest wall resection and reconstruction (CWRR) is quite challenging in surgery, due to evolution in techniques. Neoplasms of the chest wall, primary or secondary, have been considered inoperable for a long time. Thanks to evolving surgical techniques, reconstruction after extensive chest wall resection is possible with good functional and aesthetic results. Methods: In our single-center experience, seven cases of extensive CWRR for tumors were performed with a multidisciplinary approach by both thoracic and plastic surgeons...
December 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29312603/intratumoral-heterogeneity-and-tert-promoter-mutations-in-progressive-higher-grade-meningiomas
#18
Tareq A Juratli, Christian Thiede, Mara V A Koerner, Shilpa S Tummala, Dirk Daubner, Ganesh M Shankar, Erik A Williams, Maria Martinez-Lage, Silke Soucek, Katja Robel, Tristan Penson, Mechthild Krause, Steffen Appold, Matthias Meinhardt, Thomas Pinzer, Julie J Miller, Dietmar Krex, Heather A Ely, Ian M Silverman, Jason Christiansen, Gabriele Schackert, Hiroaki Wakimoto, Matthias Kirsch, Priscilla K Brastianos, Daniel P Cahill
Background: Recent studies have reported mutations in the telomerase reverse transcriptase promoter (TERTp) in meningiomas. We sought to determine the frequency, clonality and clinical significance of telomere gene alterations in a cohort of patients with progressive/higher-grade meningiomas. Methods: We characterized 64 temporally- and regionally-distinct specimens from 26 WHO grade III meningioma patients. On initial diagnoses, the meningiomas spanned all WHO grades (3 grade I, 13 grade II and 10 grade III)...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310402/a-rare-variation-of-celiac-trunk-and-hepatic-artery-complicating-pancreaticoduodenectomy-a-case-report-and-literature-review
#19
Zhou Ye, Song Ye, Dongkai Zhou, Shusen Zheng, Weilin Wang
RATIONALE: Anatomical variations of the celiac trunk and the hepatic artery are of considerable importance in hepatopancreatobiliary surgery, liver transplants, and radiological abdominal interventions. PATIENT CONCERNS: Here, we report a 57-year-old man with 2 weeks of painless progressive jaundice. Preoperative imaging and cytology brush results suggested an ampullary tumor and common hepatic artery anomaly (CTA) was reported. The patient underwent pancreaticoduodenectomy (PD)...
December 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29305118/endoscope-holders-in-cranial-neurosurgery-part-2-an-international-survey
#20
Dimitrios Paraskevopoulos, Shlomi Constantini, Jarnail Bal, Jonathan Roth
BACKGROUND: Following a prior systematic review of currently available endoscope holders (EH), we aspired to detect trends, task-specific preferences and pitfalls of EH in various cranial neuroendoscopic procedures. METHODS: A questionnaire was disseminated to members of the International Federation of Neuroendoscopy (IFNE). The questionnaire evaluated indications and pitfalls of EH in different applications, in particular, differentiating between intraventricular and skull base endoscopy, as well as sub-categories of these two main fields...
January 2, 2018: World Neurosurgery
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