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https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#1
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28297442/correlation-of-quantitative-dynamic-contrast-enhanced-mri-with-microvascular-density-in-necrotic-partial-necrotic-and-viable-liver-tumors-in-a-rabbit-model
#2
Jungwon Moon, Jae-Hun Kim, Dongil Choi, Jehoon Yang, Min Woo Lee, Yoon-La Choi, Hyunchul Rhim Md
The purpose of this study was to examine the correlation of quantitative dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) with microvessel density (MVD) in necrotic, partial necrotic, and viable tumors using a rabbit VX2 liver tumor model. Nine rabbits were used for this study. The complete necrotic area (CNA), partial necrotic area (PNA), and viable tumor area (VTA) of liver tumors were experimentally induced by radiofrequency ablation (RFA). DCE-MRI data were processed based on the extended Kety model to estimate Ktrans,ve and vp parameters...
September 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28257959/the-immune-microenvironment-genome-wide-copy-number-aberrations-and-survival-in-mesothelioma
#3
Bibhusal Thapa, Adriana Salcedo, Xihui Lin, Marzena Walkiewicz, Carmel Murone, Malaka Ameratunga, Khashyar Asadi, Siddhartha Deb, Stephen Arthur Barnett, Simon Knight, Paul Mitchell, D Neil Watkins, Paul C Boutros, Thomas John
INTRODUCTION: Results of recent clinical studies of immune checkpoint inhibitors in malignant pleural mesothelioma (MPM) have dampened initial enthusiasm. However, the immune environment and targets of these treatments such as program cell death protein 1 (PD-1) and its ligand PD-L1 have not been well characterised in MPM. Using a large cohort of patients, we investigated PD-L1 expression, immune infiltrates and genome-wide copy number status and correlated them to clinicopathological features...
February 28, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#4
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28204993/needs-of-neuro-oncological-patients-and-their-caregivers-during-the-hospitalization-and-after-discharge-results-from-a-longitudinal-study
#5
C Scaratti, M Leonardi, A Saladino, E Anghileri, M Broggi, E Lamperti, L Fariselli, R Ayadi, G Tringali, S Schiavolin
PURPOSE: The aims of this study are to identify neuro-oncological patients' and their caregivers' needs during hospitalization (T0) and at 4 months after discharge (T1); to analyze the longitudinal changes in patients' and caregivers' needs and burden; to identify correlations between patients' needs and caregivers' burden and needs. METHODS: A pilot observational longitudinal study was conducted on 94 neuro-oncological patients and their caregivers using NEQ to evaluate patients' needs, CNA, and FSQ for caregivers' needs and burden at T0 and T1...
February 15, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/28202506/recurrent-patterns-of-dna-copy-number-alterations-in-tumors-reflect-metabolic-selection-pressures
#6
Nicholas A Graham, Aspram Minasyan, Anastasia Lomova, Ashley Cass, Nikolas G Balanis, Michael Friedman, Shawna Chan, Sophie Zhao, Adrian Delgado, James Go, Lillie Beck, Christian Hurtz, Carina Ng, Rong Qiao, Johanna Ten Hoeve, Nicolaos Palaskas, Hong Wu, Markus Müschen, Asha S Multani, Elisa Port, Steven M Larson, Nikolaus Schultz, Daniel Braas, Heather R Christofk, Ingo K Mellinghoff, Thomas G Graeber
Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including (18)F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation...
February 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28193735/comprehensive-genomic-profiling-aids-in-distinguishing-metastatic-recurrence-from-second-primary-cancers
#7
Benjamin A Weinberg, Kyle Gowen, Thomas K Lee, Sai-Hong Ignatius Ou, Robert Bristow, Lauren Krill, M Isabel Almira-Suarez, Siraj M Ali, Vincent A Miller, Stephen V Liu, Samuel J Klempner
BACKGROUND: Metastatic recurrence after treatment for locoregional cancer is a major cause of morbidity and cancer-specific mortality. Distinguishing metastatic recurrence from the development of a second primary cancer has important prognostic and therapeutic value and represents a difficult clinical scenario. Advances beyond histopathological comparison are needed. We sought to interrogate the ability of comprehensive genomic profiling (CGP) to aid in distinguishing between these clinical scenarios...
February 13, 2017: Oncologist
https://www.readbyqxmd.com/read/28193567/genomic-analysis-of-adult-b-all-identifies-potential-markers-of-shorter-survival
#8
Shiven Patel, Clinton C Mason, Martha J Glenn, Christian N Paxton, Sara T South, Melissa H Cessna, Julie Asch, Erin F Cobain, Dale L Bixby, Lauren B Smith, Shalini Reshmi, Julie M Gastier-Foster, Joshua D Schiffman, Rodney R Miles
B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding genetic prognostic biomarkers are much more limited for adult patients. We identified 70 adult B-ALL patients from three institutions and performed genome-wide analysis via single nucleotide polymorphism (SNP) arrays on DNA isolated from their initial diagnostic sample and, when available, relapse bone marrow specimens to identify recurring copy number alterations (CNA)...
February 3, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28192599/impact-of-an-alternative-chromosome-17-probe-and-the-2013-american-society-of-clinical-oncology-and-college-of-american-pathologists-guidelines-on-fluorescence-in-situ-hybridization-for-the-determination-of-her2-gene-amplification-in-breast-cancer
#9
Alana R Donaldson, Shashirekha Shetty, Zhen Wang, Christine L Rivera, Bryce P Portier, G Thomas Budd, Erinn Downs-Kelly, Christopher P Lanigan, Benjamin C Calhoun
BACKGROUND: The dual-probe fluorescence in situ hybridization (FISH) assay for human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer provides an HER2:CEP17 (centromere enumeration probe for chromosome 17) ratio. Copy number alteration (CNA) in CEP17 may skew this ratio. The authors analyzed the impact of the 2013 American Society of Oncology/College of American Pathologists (ASCO/CAP) guidelines and an alternative chromosome 17 probe on HER2 status in tumor specimens with CEP17 CNA...
February 13, 2017: Cancer
https://www.readbyqxmd.com/read/28161066/genomic-profile-in-gestational-and-non-gestational-choriocarcinomas
#10
Julia Bette Homem de Mello, Priscila Daniele Ramos Cirilo, Odair Carlito Michelin, Maria Aparecida Custódio Domingues, Marilza Vieira Cunha Rudge, Silvia Regina Rogatto, Izildinha Maestá
INTRODUCTION: Gestational (GC) (derived from the placenta) and non-gestational (NGC) choriocarcinomas are trophoblastic diseases originated from abnormal proliferation of trophoblastic cells. These rare tumors share similar morphology and pathological features and differ on chemotherapy response, genetic origin and prognosis. In this study, the genomic profile of choriocarcinomas was performed according to their origin (GC or NGC) aiming to better understand these poorly characterized diseases...
February 2017: Placenta
https://www.readbyqxmd.com/read/28152688/a-new-digital-classification-schema-to-detect-treatment-variances-and-enable-value-based-payment-reforms
#11
Eric V Schultz, Kelly Choi, William Kea, Augie Smith, Cindy Kim, Matthew Axelrod, Teresa Fletcher, Matthew Love, Ruth Pe Benito, Samira Daswani, Sukhi Kaur, Kathyrn Tanenbaum, James Schaffer, Ali Hasan, Dilip Raj, Kumar Bharath Prabhu, Kiran Suryadevara, Ryan Callahan, Stuart L Goldberg
28 Background: Value based payment reforms which improve the outcome to cost ratio (paying for outcomes not for services) require detailed information on both elements. Although the digitalization of medicine via the EHR may facilitate data collection, the imprecise ICD9 and ICD10 schemas hinder analysis (eg: all breast cancers are ICD9 174.9). A more precise classification schema that accounts for biologic variances to allow analysis (and reduction) of treatment variances is needed. METHODS: We have developed a digital classification (COTA Nodal Address) based on known clinically relevant prognostic variables...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28151647/single-cell-and-single-molecule-analysis-unravels-the-multifunctionality-of-the-staphylococcus-aureus-collagen-binding-protein-cna
#12
Claire Valotteau, Valeria Prystopiuk, Giampiero Pietrocola, Simonetta Rindi, Daniele Peterle, Vincenzo De Filippis, Timothy J Foster, Pietro Speziale, Yves F Dufrêne
The collagen-binding protein Cna is a prototype cell surface protein from Staphylococcus aureus which fulfils important physiological functions during pathogenesis. While it is established that Cna binds to collagen (Cn) via the high-affinity collagen hug mechanism, whether this protein is engaged in other ligand-binding mechanisms is poorly understood. Here, we use atomic force microscopy to demonstrate that Cna mediates attachment to two structurally and functionally different host proteins, i.e., the complement system protein C1q and the extracellular matrix protein laminin (Lam), through binding mechanisms that differ from the collagen hug...
February 28, 2017: ACS Nano
https://www.readbyqxmd.com/read/28126143/-copy-number-alterations-in-adult-patients-with-mature-b-acute-lymphoblastic-leukemia-treated-with-specific-immunochemotherapy
#13
Jordi Ribera, Lurdes Zamora, Olga García, Jesús-María Hernández-Rivas, Eulàlia Genescà, Josep-Maria Ribera
BACKGROUND AND OBJECTIVE: Unlike Burkitt lymphoma, molecular abnormalities other than C-MYC rearrangements have scarcely been studied in patients with mature B acute lymphoblastic leukemia (B-ALL). The aim of this study was to analyze the frequency and prognostic significance of copy number alterations (CNA) in genes involved in lymphoid differentiation, cell cycle and tumor suppression in adult patients with B-ALL. PATIENTS AND METHODS: We have analyzed by multiplex ligation-dependent probe amplification the genetic material from bone marrow at diagnosis from 25 adult B-ALL patients treated with rituximab and specific chemotherapy...
December 2, 2016: Medicina Clínica
https://www.readbyqxmd.com/read/28125801/genome-wide-copy-number-aberrations-and-her2-and-fgfr1-alterations-in-primary-breast-cancer-by-molecular-inversion-probe-microarray
#14
Hui Chen, Rajesh R Singh, Xinyan Lu, Lei Huo, Hui Yao, Kenneth Aldape, Ronald Abraham, Shumaila Virani, Meenakshi Mehrotra, Bal Mukund Mishra, Alex Bousamra, Constance Albarracin, Yun Wu, Sinchita Roy-Chowdhuri, Rashmi Kanagal Shamanna, Mark J Routbort, L Jeffrey Medeiros, Keyur P Patel, Russell Broaddus, Aysegul Sahin, Rajyalakshmi Luthra
Breast cancer remains the second leading cause of cancer-related death in women despite stratification based on standard hormonal receptor (HR) and HER2 testing. Additional prognostic markers are needed to improve breast cancer treatment. Chromothripsis, a catastrophic genome rearrangement, has been described recently in various cancer genomes and affects cancer progression and prognosis. However, little is known about chromothripsis in breast cancer. To identify novel prognostic biomarkers in breast cancer, we used molecular inversion probe (MIP) microarray to explore genome-wide copy number aberrations (CNA) and breast cancer-related gene alterations in DNA extracted from formalin-fixed paraffin-embedded tissue...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28124185/mouse-models-of-breast-cancer-share-amplification-and-deletion-events-with-human-breast-cancer
#15
Jonathan Rennhack, Briana To, Harrison Wermuth, Eran R Andrechek
Breast tumor heterogeneity has been well documented through the use of multiplatform -omic studies in human tumors. However, there is no integrative database to capture the heterogeneity within mouse models of breast cancer. This project identifies genomic copy number alterations (CNAs) in 600 tumors across 27 major mouse models of breast cancer through the application of a predictive algorithm to publicly available gene expression data. It was found that despite the presence of strong oncogenic drivers in most mouse models, CNAs are extremely common but heterogeneous both between models and within models...
March 2017: Journal of Mammary Gland Biology and Neoplasia
https://www.readbyqxmd.com/read/28113239/intsim-an-integrated-simulator-of-next-generation-sequencing-data
#16
Xiguo Yuan, Junying Zhang, Liying Yang
OBJECTIVE: Next-generation sequencing data has been widely used for DNA variant discovery and tumor study through computational tools. Effective simulation of such data with many realistic features is very necessary for testing existing tools and guiding the development of new tools. METHODS: We present an integrated simulation system, IntSIM, to simulate common DNA variants and to generate sequencing reads for mixture genomes. IntSIM has three novel features in comparison with other simulation programs: (1) it is able to simulate both germline and somatic variants in the same sequence, (2) it deals with tumor purity so as to generate reads corresponding to heterogeneous genomes and also produce tumor-normal matched samples, (3) it simulates correlations among SNPs, among CNVs/CNAs based on HMM models trained from real sequencing genomes, and can simulates broad and focal CNV/CNA events...
April 29, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28108046/rules-of-performance-in-the-nursing-home-a-grounded-theory-of-nurse-cna-communication
#17
Connie Madden, Margaret Clayton, Heather E Canary, Gail Towsley, Kristin Cloyes, Dale Lund
This study offers an initial theoretical understanding of nurse-CNA communication processes from the perspectives of nurses and CNAs who are providing direct care to residents in nursing homes. A grounded theory approach provided an understanding of nurse-CNA communication process within the complexities of the nursing home setting. Four themes (maintaining information flow, following procedure, fostering collegiality, and showing respect) describe the "rules of performance" that intertwine in nuanced relationships to guide nurse-CNA communication processes...
January 17, 2017: Geriatric Nursing
https://www.readbyqxmd.com/read/28106018/cardioneuroablation-in-the-treatment-of-neurally-mediated-reflex-syncope-a-review-of-the-current-literature
#18
Tolga Aksu, Tümer Erdem Güler, Serdar Bozyel, Kazım Serhan Özcan, Kıvanç Yalın, Ferit Onur Mutluer
OBJECTIVE: An imbalance between parasympathetic and sympathetic tone is a main cause of neurally mediated reflex syncope (NMRS). These patients may be very symptomatic and the condition may require cardiac pacemaker implantation. Cardioneuroablation (CNA) is a relatively novel technique based on radiofrequency ablation of vagal ganglia that can be used in treatment of NMRS. The aim of this analysis was to compare potential role of CNA in patients with NMRS. METHODS: In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement, literature search was conducted using the keywords "cardioneuroablation," "vagal denervation," "reflex syncope," "vagal ablation," and "ganglionic plexi ablation...
December 2017: Türk Kardiyoloji Derneği Arşivi: Türk Kardiyoloji Derneğinin Yayın Organıdır
https://www.readbyqxmd.com/read/28102477/potential-new-mechanisms-of-pro-arrhythmia-in-arrhythmogenic-cardiomyopathy-focus-on-calcium-sensitive-pathways
#19
REVIEW
C J M van Opbergen, M Delmar, T A B van Veen
Arrhythmogenic cardiomyopathy, or its most well-known subform arrhythmogenic right ventricular cardiomyopathy (ARVC), is a cardiac disease mainly characterised by a gradual replacement of the myocardial mass by fibrous and fatty tissue, leading to dilatation of the ventricular wall, arrhythmias and progression towards heart failure. ARVC is commonly regarded as a disease of the intercalated disk in which mutations in desmosomal proteins are an important causative factor. Interestingly, the Dutch founder mutation PLN R14Del has been identified to play an additional, and major, role in ARVC patients within the Netherlands...
March 2017: Netherlands Heart Journal
https://www.readbyqxmd.com/read/28093192/spectrum-of-mutations-in-leiomyosarcomas-identified-by-clinical-targeted-next-generation-sequencing
#20
Paul J Lee, Naomi S Yoo, Ian S Hagemann, John D Pfeifer, Catherine E Cottrell, Haley J Abel, Eric J Duncavage
Recurrent genomic mutations in uterine and non-uterine leiomyosarcomas have not been well established. Using a next generation sequencing (NGS) panel of common cancer-associated genes, 25 leiomyosarcomas arising from multiple sites were examined to explore genetic alterations, including single nucleotide variants (SNV), small insertions/deletions (indels), and copy number alterations (CNA). Sequencing showed 86 non-synonymous, coding region somatic variants within 151 gene targets in 21 cases, with a mean of 4...
January 14, 2017: Experimental and Molecular Pathology
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