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next generate sequencing AND cancer

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https://www.readbyqxmd.com/read/29035575/hetfhmm-a-novel-approach-to-infer-tumor-heterogeneity-using-factorial-hidden-markov-models
#1
Mohammad S Rahman, Ann E Nicholson, Gholamreza Haffari
Cancer arises from successive rounds of mutations, resulting in tumor cells with different somatic mutations known as clones. Drug responsiveness and therapeutics of cancer depend on the accurate detection of clones in a tumor sample. Recent research has considered inferring clonal composition of a tumor sample using computational models based on short read data of the sample generated using next-generation sequencing (NGS) technology. Short reads (segmented DNA parts of different tumor cells) are noisy; therefore, inferring the clones and their mutations from the data is a difficult and complex problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29033976/conffuse-high-confidence-fusion-gene-detection-across-tumor-entities
#2
Zhiqin Huang, David T W Jones, Yonghe Wu, Peter Lichter, Marc Zapatka
Background: Fusion genes play an important role in the tumorigenesis of many cancers. Next-generation sequencing (NGS) technologies have been successfully applied in fusion gene detection for the last several years, and a number of NGS-based tools have been developed for identifying fusion genes during this period. Most fusion gene detection tools based on RNA-seq data report a large number of candidates (mostly false positives), making it hard to prioritize candidates for experimental validation and further analysis...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#3
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29030356/cell-cycle-and-dna-damage-response-pathway-is-involved-in-leptomeningeal-metastasis-of-non-small-cell-lung-cancer
#4
Yun Fan, Xuehua Zhu, Yan Xu, Xuesong Lu, Yanjun Xu, Mengzhao Wang, Haiyan Xu, Jingyan Ding, Xin Ye, Luo Fang, Zhiyu Huang, Lei Gong, Hongyang Lu, Weimin Mao, Min Hu
PURPOSE: Leptomeningeal metastases (LM) is a detrimental complication of non-small cell lung cancer (NSCLC) and associated with poor prognosis. However, the underlying mechanisms of the metastasis process are still poorly understood. EXPERIMENTAL DESIGN: We performed next-generation panel sequencing of primary tumor tissue, cerebrospinal fluid (CSF) and matched normal controls from epidermal growth factor receptor (EGFR) mutation-positive NSCLC patients with LM...
October 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29029730/assessing-the-diversity-of-rodent-borne-viruses-exploring-of-high-throughput-sequencing-and-classical-amplification-sequencing-approaches
#5
Stephan Drewes, Petra Straková, Jan F Drexler, Jens Jacob, Rainer G Ulrich
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/29028645/an-update-on-the-status-of-molecular-testing-for-the-indeterminate-thyroid-nodule-and-risk-stratification-of-differentiated-thyroid-cancer
#6
Kristina J Nicholson, Linwah Yip
PURPOSE OF REVIEW: Correct identification of malignancy in cytologically indeterminate thyroid nodules is a diagnostic challenge, leading to potentially unnecessary surgery in patients for whom final histology is benign. Similarly, many patients with differentiated thyroid cancer (DTC) undergo aggressive surgical management of tumors, which may ultimately have low-risk histologic features. Use of molecular testing strategies can aid in both the diagnosis of indeterminate thyroid nodules and preoperative risk stratification of DTC...
October 11, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29028368/a-window-into-clinical-next-generation-sequencing-based-oncology-testing-practices
#7
Rakesh Nagarajan, Angela N Bartley, Julia A Bridge, Lawrence J Jennings, Suzanne Kamel-Reid, Annette Kim, Alexander J Lazar, Neal I Lindeman, Joel Moncur, Alex J Rai, Mark J Routbort, Patricia Vasalos, Jason D Merker
CONTEXT: - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. OBJECTIVE: - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. DESIGN: - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing...
October 13, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29027617/zebrafish-as-a-model-to-study-neuroblastoma-development
#8
REVIEW
Mattie J Casey, Rodney A Stewart
Neuroblastoma is a pediatric solid tumor arising from embryonic neural crest progenitor cells that normally generate the peripheral sympathetic nervous system. As such, the location of neuroblastoma tumors is correlated with the distribution of major post-ganglionic clusters throughout the sympathetic chain, with the highest incidence in the adrenal medulla or lumbar sympathetic ganglia (~65%). Neuroblastoma is an enigmatic tumor that can spontaneously regress with minimal treatment or become highly metastatic and develop resistance to aggressive treatments, including radiation and high-dose chemotherapy...
October 13, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29027537/optimal-detection-of-clinically-relevant-mutations-in-colorectal-carcinoma-sample-pooling-overcomes-intra-tumoral-heterogeneity
#9
Andrew C Nelson, Jamie Boone, David Cartwright, Bharat Thyagarajan, Robyn Kincaid, Aaron P Lambert, Kylene Karnuth, Christine Henzler, Sophia Yohe
Intra-tumoral genomic heterogeneity is a well-established biologic property of human malignancies with emerging roles in cancer progression and therapy resistance. However, its impact on the clinical utility of genomic testing in patient management remains unclear. Furthermore, best practices to account for heterogeneity in the provision of highly accurate, clinically valid molecular testing have yet to be firmly established. Genomic biomarkers for the management of colorectal carcinoma are both well-established (ie, KRAS, NRAS) and emerging (BRAF, PIK3CA, and others) in respect to therapy selection and clinical trial eligibility...
October 13, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29025599/constitutional-mosaicism-of-a-de-novo-tp53-mutation-in-a-patient-with-bilateral-choroid-plexus-carcinoma
#10
Joanna Trubicka, Iwona Filipek, Iwanowski Piotr, Małgorzata Rydzanicz, Wiesława Grajkowska, Dorota Piekutowska-Abramczuk, Krystyna Chrzanowska, Agnieszka Karkucińska-Więckowska, Katarzyna Iwanicka-Pronicka, Maciej Pronicki, Maria Łastowska, Rafał Płoski, Bożenna Dembowska-Bagińska
Choroid plexus tumors (CPT) constitute 2%-5% of all pediatric brain tumors and include high grade choroid plexus carcinoma (CPC). About 40% of CPC patients harbor germline TP53 mutations, associated with diminished survival rates. However, the number of TP53 carriers might be underestimated due to suboptimal ability of Sanger sequencing to identify mosaicism. We describe an 18-month-old boy with ultra-rare, bilateral disseminated CPC and negative family history of cancer. Next generation sequencing (NGS) revealed constitutional mosaicism of de novo TP53 mutation, which was barely detectable by Sanger sequencing...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29025590/identification-of-pathogenic-retrotransposon-insertions-in-cancer-predisposition-genes
#11
Yaping Qian, Debora Mancini-DiNardo, Thaddeus Judkins, Hannah C Cox, Krystal Brown, Maria Elias, Nanda Singh, Courtney Daniels, Jayson Holladay, Bradford Coffee, Karla R Bowles, Benjamin B Roa
Cancer risks have been previously reported for some retrotransposon element (RE) insertions; however, detection of these insertions is technically challenging and very few oncogenic RE insertions have been reported. Here we evaluate RE insertions identified during hereditary cancer genetic testing using a comprehensive testing strategy. Individuals who had single-syndrome or pan-cancer hereditary cancer genetic testing from February 2004 to March 2017 were included. RE insertions were identified using Sanger sequencing, Next Generation Sequencing, or multiplex quantitative PCR, and further characterized using targeted PCR and sequencing analysis...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#12
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29020732/detection-of-germline-mutations-in-patients-with-epithelial-ovarian-cancer-using-multi-gene-panels-beyond-brca1-2
#13
Kyung Jin Eoh, Ji Eun Kim, Hyung Seok Park, Seung-Tae Lee, Ji Soo Park, Jung Woo Han, Jung-Yun Lee, Sunghoon Kim, Sang Wun Kim, Jae Hoon Kim, Young Tae Kim, Eun Ji Nam
Purpose: Next-generation sequencing (NGS) allows simultaneous sequencing of multiple cancer susceptibility genes and may represent a more efficient and less expensive approach than sequential testing. We assessed the frequency of germline mutations in individuals with epithelial ovarian cancer (EOC), using multi-gene panels and NGS. Materials and Methods: Patients with EOC (n=117) with/without a family history of breast or ovarian cancer were recruited consecutively, from March 2016 to December 2016...
September 27, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/29020724/chromothripsis-in-treatment-resistance-in-multiple-myeloma
#14
Kyoung Joo Lee, Ki Hong Lee, Kyong-Ah Yoon, Ji Yeon Sohn, Eunyoung Lee, Hyewon Lee, Hyeon-Seok Eom, Sun-Young Kong
Multiple myeloma (MM) is a malignant disease caused by an abnormal proliferation of plasma cells, of which the prognostic factors include chromosomal abnormality, β-2 microglobulin, and albumin. Recently, the term chromothripsis has emerged, which is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event. Many studies have shown an association of chromothripsis with the prognosis in several cancers; however, few studies have investigated it in MM. Here, we studied the association between chromothripsis-like patterns and treatment resistance or prognosis...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020660/identification-of-twenty-nine-novel-germline-unclassified-variants-of-brca1-and-brca2-genes-in-1400-italian-individuals
#15
Concetta Santonocito, Margherita Scapaticci, Donatella Guarino, Andrea Bartolini, Angelo Minucci, Paola Concolino, Giovanni Scambia, Ida Paris, Ettore Capoluongo
OBJECTIVES: Breast and/or ovarian cancers are complex multifactorial diseases caused by interaction of both genetic and non-genetic factors and characterized by predisposition to inheritance. BRCA1 and BRCA2 genes are the most clinically involved with these kinds of cancer and the spectrum of variants affecting these genes is very wide. In fact, point variants, large or small insertions/deletions, genomic rearrangements can be found in these patients, although a large number of variants with uncertain biological and clinical significance continues to be identified...
October 8, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/29018623/voomdda-discovery-of-diagnostic-biomarkers-and-classification-of-rna-seq-data
#16
Gokmen Zararsiz, Dincer Goksuluk, Bernd Klaus, Selcuk Korkmaz, Vahap Eldem, Erdem Karabulut, Ahmet Ozturk
RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data...
2017: PeerJ
https://www.readbyqxmd.com/read/28994108/value-of-a-molecular-screening-program-to-support-clinical-trial-enrollment-in-asian-cancer-patients-the-integrated-molecular-analysis-of-cancer-imac-study
#17
Valerie Heong, Nicholas L Syn, Xiao Wen Lee, Nur Sabrina Sapari, Xue Qing Koh, Zul Fazreen Adam Isa, Joey Sy Lim, Diana Lim, Brendan Pang, Yee Liang Thian, Lai Kuan Ng, Andrea L Wong, Ross Andrew Soo, Wei Peng Yong, Cheng Ean Chee, Soo-Chin Lee, Boon-Cher Goh, Richie Soong, David S P Tan
The value of precision oncology initiatives in Asian contexts remains unresolved. Here we review the institutional implementation of prospective molecular screening to facilitate accrual of patients into biomarker-driven clinical trials, and to explore the mutational landscape of advanced tumors occurring in a prospective cohort of Asian patients (n = 396) with diverse cancer types. Next-generation sequencing (NGS) and routine clinicopathological assays such as immunohistochemistry, copy number analysis, and in situ hybridization tests were performed on tumor samples...
October 9, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28993866/cdh1-mutation-screen-in-a-brca1-2-negative-familial-breast-ovarian-cancer-cohort
#18
Frederik Stuebs, Simone Heidemann, Almuth Caliebe, Christoph Mundhenke, Norbert Arnold
PURPOSE: Mutations in the CDH1 gene are linked both to diffuse gastric cancer and invasive lobular carcinoma (ILC). A high mutation rate is found in families fulfilling the diagnostic criteria for hereditary diffuse gastric cancer. Aim of this study was to clarify whether or not there is a significant contribution of CDH1 mutations in hereditary breast-/ovarian cancer (HBOC). METHODS: Ninety-seven unrelated probands fulfilling the diagnostic criteria for HBOC (96 affected, 1 unaffected) but tested negative for pathogenic BRCA1/2 mutations were screened for CDH1 mutations by denaturing high performance liquid chromatography (DHPLC) and subsequent Sanger sequencing of suspicious and positive DHPLC results...
October 9, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28989037/lung-cancer-patients-with-germline-mutations-detected-by-next-generation-sequencing-and-or-liquid-biopsy
#19
Takehito Shukuya, Sandipkumar Patel, Kate Shane-Carson, Kai He, Erin M Bertino, Konstantin Shilo, Gregory A Otterson, David P Carbone
No abstract text is available yet for this article.
October 5, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28987144/cancer-associated-fibroblasts-cafs-are-activated-in-cutaneous-basal-cell-carcinoma-and-in-the-peritumoural-skin
#20
Silje Haukali Omland, Erika Elgstrand Wettergren, Tobias Mourier, Anders Johannes Hansen, Maria Asplund, Sarah Mollerup, Robert Robert
BACKGROUND: Cutaneous basal cell carcinoma (BCC) is the commonest cancer worldwide. BCC is locally invasive and the surrounding stromal microenvironment is pivotal for tumourigenesis. Cancer associated fibroblasts (CAFs) in the microenvironment are essential for tumour growth in a variety of neoplasms but their role in BCC is poorly understood. METHODS: Material included facial BCC and control skin from the peritumoural area and from the buttocks. With next-generation sequencing (NGS) we compared mRNA expression between BCC and peritumoural skin...
October 7, 2017: BMC Cancer
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