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https://www.readbyqxmd.com/read/28339163/next-generation-sequencing-of-urine-specimens-a-novel-platform-for-genomic-analysis-in-patients-with-non-muscle-invasive-urothelial-carcinoma-treated-with-bacille-calmette-gu%C3%A3-rin
#1
Sasinya N Scott, Irina Ostrovnaya, Caroline M Lin, Nancy Bouvier, Bernard H Bochner, Gopakumar Iyer, David Solit, Michael F Berger, Oscar Lin
BACKGROUND: Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment...
March 24, 2017: Cancer
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#2
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28331883/practical-no-gold-standard-evaluation-framework-for-quantitative-imaging-methods-application-to-lesion-segmentation-in-positron-emission-tomography
#3
Abhinav K Jha, Esther Mena, Brian Caffo, Saeed Ashrafinia, Arman Rahmim, Eric Frey, Rathan M Subramaniam
Recently, a class of no-gold-standard (NGS) techniques have been proposed to evaluate quantitative imaging methods using patient data. These techniques provide figures of merit (FoMs) quantifying the precision of the estimated quantitative value without requiring repeated measurements and without requiring a gold standard. However, applying these techniques to patient data presents several practical difficulties including assessing the underlying assumptions, accounting for patient-sampling-related uncertainty, and assessing the reliability of the estimated FoMs...
January 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28321501/visualization-of-tumor-heterogeneity-by-in-situ-padlock-probe-technology-in-colorectal-cancer
#4
Amin El-Heliebi, Karl Kashofer, Julia Fuchs, Stephan W Jahn, Christian Viertler, Andrija Matak, Peter Sedlmayr, Gerald Hoefler
Tumor heterogeneity is considered a major cause for therapy resistance in colorectal cancer. Sub-populations of cells with different genetic alterations may exist in spatially distinct areas. Upon therapy, resistant sub-clones may enrich and ultimately lead to disease progression. Although ample data are available on tumors which are heterogeneous on a morphological level, only little is known about morphologically homogeneous tumors. We aimed to investigate if morphologically homogeneous colorectal cancer can harbor a heterogeneous genetic landscape...
March 20, 2017: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28320758/tumor-cell-free-dna-copy-number-instability-predicts-therapeutic-response-to-immunotherapy
#5
Glen J Weiss, Julia Beck, Donald P Braun, Kristen Bornemann-Kolatzki, Heather Barilla, Rhiannon Cubello, Walter Quan, Ashish Sangal, Vivek Khemka, Jordan Waypa, William M Mitchell, Howard Urnovitz, Ekkehard Schütz
PURPOSE: Chromosomal instability is a fundamental property of cancer, which can be quantified by Next Generation Sequencing (NGS) from plasma/serum derived cell-free DNA (cfDNA). We hypothesized that cfDNA could be used as a real time surrogate for imaging analysis of disease status as a function of response to immunotherapy and as a more reliable tool than tumor biomarkers. EXPERIMENTAL DESIGN: Plasma cfDNA sequences from 56 patients with diverse advanced cancers, were prospectively collected and analyzed in a single-blinded study for copy number variations, expressed as a quantitative chromosomal number instability (CNI) score versus 126 non-cancer controls in a training set of 23 and a blinded validation set of 33...
March 20, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28315974/inherited-dna-repair-gene-mutations-detected-by-tumor-next-generation-sequencing-in-urinary-tract-cancers
#6
Sumati Gupta, Samantha Greenberg, Jade Grimmett, David Gaston, Neeraj Agarwal, William Lowrance, Joshua Schiffman, Wendy Kohlmann
Interpretation of next-generation sequencing (NGS) of tumor tissue in patients with advanced Urinary Tract Cancer (UTC) is performed to guide treatment selection but may reveal pathogenic variants with germline implications. We identified three patients with UTC with unexpected germline DNA repair gene mutations. Specific testing for these was prompted by the detection of these mutations by tumor NGS. All three patients were nonsmokers with a strong family history of cancer. Two patients had upper tract UTC with age at diagnosis in the 40 s...
March 18, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28306219/characterization-of-a-novel-pold1-missense-founder-mutation-in-a-spanish-population
#7
Rosario Ferrer-Avargues, Virginia Díez-Obrero, Ester Martín-Tomás, Eva Hernández-Illán, María-Isabel Castillejo, Alan Codoñer-Alejos, Víctor-Manuel Barberá, Ana-Beatriz Sánchez-Heras, Ángel Segura, María-José Juan, Isabel Tena, Adela Castillejo, José-Luis Soto
BACKGROUND: We identified a new and a recurrent POLD1 mutation associated with predisposition to colorectal cancer (CRC). We characterized the molecular and clinical nature of the potential POLD1 founder mutation in families from Valencia (Spain). METHODS: Clinical and molecular data were collected from 4 independent families known to have a POLD1 Leu474Pro mutation. To establish its founder effect, haplotype construction was performed using 14 flanking POLD1 polymorphic markers...
March 17, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28304377/establishment-of-a-novel-cellular-model-for-myxofibrosarcoma-heterogeneity
#8
Birgit Lohberger, Nicole Stuendl, Andreas Leithner, Beate Rinner, Stefan Sauer, Karl Kashofer, Bernadette Liegl-Atzwanger
Human cancers frequently display substantial intra-tumoural heterogeneity in virtually all distinguishable phenotypic features, such as cellular morphology, gene expression, and metastatic potential. In order to investigate tumour heterogeneity in myxofibrosarcoma, we established a novel myxofibrosarcoma cell line with two well defined sub-clones named MUG-Myx2a and MUG-Myx2b. The parental tumour tissue and both MUG-Myx2 cell lines showed the same STR profile. The fact that MUG-Myx2a showed higher proliferation activity, faster migration and enhanced tumourigenicity was of particular interest...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303491/changing-the-therapeutic-landscape-in-non-small-cell-lung-cancers-the-evolution-of-comprehensive-molecular-profiling-improves-access-to-therapy
#9
REVIEW
Joshua K Sabari, Fernando Santini, Isabella Bergagnini, W Victoria Lai, Kathryn C Arbour, Alexander Drilon
Targeting genomic alterations has led to a paradigm shift in the treatment of patients with lung cancer. In an effort to better identify potentially actionable alterations that may predict response to FDA-approved and or investigational therapies, many centers have migrated towards performing targeted exome sequencing in patients with stage IV disease. The implementation of next-generation sequencing (NGS) in the evaluation of tumor tissue from patients with NSCLC has led to the discovery of targetable alterations in tumors that previously had no known actionable targets by less comprehensive profiling...
April 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28302568/mutational-profile-from-targeted-ngs-predicts-survival-in-ldct-screening-detected-lung-cancers
#10
Carla Verri, Cristina Borzi, Todd Holscher, Matteo Dugo, Andrea Devecchi, Katherine Drake, Stefano Sestini, Paola Suatoni, Elisa Romeo, Gabriella Sozzi, Ugo Pastorino, Mattia Boeri
BACKGROUND: The issue of overdiagnosis in low-dose computed tomography (LDCT)-screening trials could be addressed by the development of complementary biomarkers able to improve detection of aggressive disease. The mutation profile of LDCT screening-detected lung tumours is currently unknown. METHODS: Targeted next-generation sequencing was performed in 94 LDCT screening-detected lung tumours. Associations with clinicopathologic features, survival and the risk profile of a plasma microRNA signature classifier (MSC) were analyzed...
March 13, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28297627/clinical-and-technical-aspects-of-genomic-diagnostics-for-precision-oncology
#11
Yuri Sheikine, Frank C Kuo, Neal I Lindeman
The emergence of precision medicine has been predicated on significant recent advances in diagnostic technology, particularly the advent of next-generation sequencing (NGS). Although the chemical technology underlying NGS is complex, and the computational biology expertise required to build systems to facilely interpret the results is highly specialized, the variables involved in designing and deploying a genomic testing program for cancer can be readily understood and applied by understanding several basic considerations...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28294317/the-spectrum-of-brca-mutations-and-characteristics-of-brca-associated-breast-cancers-in-china-screening-of-2991-patients-and-1043-controls-by-next-generation-sequencing
#12
Guan-Tian Lang, Jin-Xiu Shi, Xin Hu, Chen-Hui Zhang, Ling Shan, Chuan-Gui Song, Zhi-Gang Zhuang, A-Yong Cao, Hong Ling, Ke-Da Yu, Li Shan, Meng-Hong Sun, Xiao-Yan Zhou, Wei Huang, Zhi-Ming Shao
To characterize the prevalence of BRCA mutations and characteristics of BRCA carriers in China and to update the clinical recommendations for BRCA testing, we conducted a wide screen for BRCA mutations using next-generation sequencing (NGS). A total of 4,034 Chinese subjects were screened for germline BRCA1/2 mutations, including 2,991 breast cancer patients and 1,043 healthy individuals from the community enrolled as controls. We developed an NGS-based approach to perform BRCA1/2 screening. BRCA mutations were identified in 9...
March 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28283903/detection-of-esr1-mutations-in-plasma-and-tumors-from-metastatic-breast-cancer-patients-using-next-generation-sequencing
#13
Takehiro Yanagawa, Naofumi Kagara, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: Liquid biopsy using digital PCR (dPCR) has been widely used for the screening of ESR1 mutations, since they are frequently identified in the hotspot. However, dPCR is limited to the known mutations. Therefore, we aimed to analyze the utility of next-generation sequencing (NGS) to discover novel ESR1 mutations. METHODS: Whole exon sequencing of the ESR1 gene using NGS was performed in 16 primary and 47 recurrent tumor samples and 38 plasma samples from hormone receptor-positive metastatic breast cancer patients...
March 10, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28281147/molecular-tumor-boards-ethical-issues-in-the-new-era-of-data-medicine
#14
Henri-Corto Stoeklé, Marie-France Mamzer-Bruneel, Charles-Henry Frouart, Christophe Le Tourneau, Pierre Laurent-Puig, Guillaume Vogt, Christian Hervé
The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with "genomic medicine" nor with "precision medicine", but with "data medicine" (DM) (big data, data mining). The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The "transformation" of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision of care...
March 9, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28280620/potential-actionable-targets-in-appendiceal-cancer-detected-by-immunohistochemistry-fluorescent-in-situ-hybridization-and-mutational-analysis
#15
Erkut Borazanci, Sherri Z Millis, Jeffery Kimbrough, Nancy Doll, Daniel Von Hoff, Ramesh K Ramanathan
BACKGROUND: Appendiceal cancers are rare and consist of carcinoid, mucocele, pseudomyxoma peritonei (PMP), goblet cell carcinoma, lymphoma, and adenocarcinoma histologies. Current treatment involves surgical resection or debulking, but no standard exists for adjuvant chemotherapy or treatment for metastatic disease. METHODS: Samples were identified from approximately 60,000 global tumors analyzed at a referral molecular profiling CLIA-certified laboratory. A total of 588 samples with appendix primary tumor sites were identified (male/female ratio of 2:3; mean age =55)...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28280605/next-generation-sequencing-identifies-interactome-signatures-in-relapsed-and-refractory-metastatic-colorectal-cancer
#16
Benny Johnson, Laurence Cooke, Daruka Mahadevan
BACKGROUND: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. METHODS: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28279308/detection-of-somatic-variants-in-peripheral-blood-lymphocytes-using-a-next-generation-sequencing-multigene-pan-cancer-panel
#17
Bradford Coffee, Hannah C Cox, John Kidd, Scott Sizemore, Krystal Brown, Susan Manley, Debora Mancini-DiNardo
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%...
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28277144/molecular-tests-potentially-improving-hpv-screening-and-genotyping-for-cervical-cancer-prevention
#18
Ana Gradíssimo, Robert D Burk
Human papillomavirus (HPV)-related cancers can be averted by type-specific vaccination (primary prevention) and/or through detection and ablation of precancerous cervical lesions (secondary prevention). This review presents current challenges to cervical cancer screening programs, focusing on recent molecular advances in HPV testing and potential improvements on risk stratification. Areas covered: High-risk (HR)-HPV DNA detection has been progressively incorporated into cervix cancer prevention programs based on its increased sensitivity...
February 20, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28276747/proteogenomic-studies-on-cancer-drug-resistance-towards-biomarker-discovery-and-target-identification
#19
Shuyue Fu, Xiang Liu, Maochao Luo, Ke Xie, Edouard C Nice, Haiyuan Zhang, Canhua Huang
Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment...
March 6, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28275538/analysis-of-significantly-mutated-genes-as-a-clinical-tool-for-the-diagnosis-in-a-case-of-lung-cancer
#20
Yoshihiro Miyashita, Yosuke Hirotsu, Toshiharu Tsutsui, Seishi Higashi, Yusuke Sogami, Yumiko Kakizaki, Taichiro Goto, Kenji Amemiya, Toshio Oyama, Masao Omata
Bronchoendoscopic examination is not necessarily comfortable procedure and limited by its sensitivity, depending on the location and size of the tumor lesion. Patients with a non-diagnostic bronchoendoscopic examination often undergo further invasive examinations. Non-invasive diagnostic tool of lung cancer is desired. A 72-year-old man had a 3.0 cm × 2.5 cm mass lesion in the segment B1 of right lung. Cytological examination of sputum, bronchial washing and curetted samples were all "negative". We could confirm a diagnosis of lung cancer after right upper lung lobe resection pathologically, and also obtained concordant results by genomic analysis using cytological negative samples from airways collected before operation...
2017: Respiratory Medicine Case Reports
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