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https://www.readbyqxmd.com/read/29770616/prevalence-of-germline-brca-mutations-among-women-with-carcinoma-of-the-peritoneum-or-fallopian-tube
#1
Min Chul Choi, Jin Sik Bae, Sang Geun Jung, Hyun Park, Won Duk Joo, Seung Hun Song, Chan Lee, Ji Ho Kim, Ki Chan Lee, Sunghoon Lee, Je Ho Lee
OBJECTIVE: The aim of the present study was to assess the frequency of germline mutations in patients with peritoneal carcinoma (PC) or the fallopian tube carcinoma (FTC), using a multi-gene panel. METHODS: Twenty-six patients diagnosed with either PC or FTC between January 2013 and December 2016 were recruited consecutively. Germline DNA was sequenced using a 6-gene next generation sequencing (NGS) panel following genetic counseling. Surgico-medical information was obtained from hospital records...
March 26, 2018: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/29769598/germline-mutation-in-the-tp53-gene-in-uveal-melanoma
#2
Nikola Hajkova, Jan Hojny, Kristyna Nemejcova, Pavel Dundr, Jan Ulrych, Katerina Jirsova, Johana Glezgova, Ivana Ticha
We performed comprehensive molecular analysis of five cases of metastasizing uveal malignant melanoma (UM) (fresh-frozen samples) with an NGS panel of 73 genes. A likely pathogenic germline TP53 mutation c.760A > G (p.I254V) was found in two tumor samples and matched nontumor tissue. In three cases, pathogenic BAP1 mutation was detected together with germline missense variants of uncertain significance in ATM. All cases carried recurrent activating GNAQ or GNA11 mutation. Moreover, we analyzed samples from another 16 patients with primary UM by direct Sanger sequencing focusing only on TP53 coding region...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29765524/cross-platform-comparison-for-the-detection-of-ras-mutations-in-cfdna-ddpcr-biorad-detection-assay-beaming-assay-and-ngs-strategy
#3
Jessica Garcia, Julien Forestier, Eric Dusserre, Anne-Sophie Wozny, Florence Geiguer, Patrick Merle, Claire Tissot, Carole Ferraro-Peyret, Frederick S Jones, Daniel L Edelstein, Valérie Cheynet, Claire Bardel, Gaelle Vilchez, Zhenyu Xu, Pierre Paul Bringuier, Marc Barritault, Karen Brengle-Pesce, Marielle Guillet, Marion Chauvenet, Brigitte Manship, Marie Brevet, Claire Rodriguez-Lafrasse, Valérie Hervieu, Sébastien Couraud, Thomas Walter, Léa Payen
CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764807/predicting-the-presence-of-oral-squamous-cell-carcinoma-using-commonly-dysregulated-microrna-in-oral-swirls
#4
Tami Yap, Kendrick Koo, Lesley Cheng, Laura J Vella, Andrew F Hill, Eric C Reynolds, Alf L Nastri, Nicola Cirillo, Christine A Seers, Michael McCullough
Oral swirls are a noninvasive, rapidly collected source of salivary microRNA potentially useful in the early detection of disease states, particularly oral squamous cell carcinoma (OSCC). The aim of this study was to predict the presence of oral squamous cell carcinoma using a panel of OSCC-related dysregulated microRNA found in oral swirls, identified jointly in data from formalin-fixed paraffin embedded (FFPE) and fresh frozen specimens. Next generation sequencing (NGS) was used to determine microRNA fold changes in FFPE OSCC specimens relative to histologically normal epithelium...
May 15, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29764005/identification-of-novel-functional-variants-of-sin3a-and-srsf1-among-somatic-variants-in-acute-myeloid-leukemia-patients
#5
Jae-Woong Min, Youngil Koh, Dae-Yoon Kim, Hyung-Lae Kim, Jeong A Han, Yu-Jin Jung, Sung-Soo Yoon, Sun Shim Choi
The advent of massively parallel sequencing, also called nextgeneration sequencing (NGS), has dramatically influenced cancer genomics by accelerating the identification of novel molecular alterations. Using a whole genome sequencing (WGS) approach, we identified somatic coding and noncoding variants that may contribute to leukemogenesis in 11 adult Korean acute myeloid leukemia (AML) patients, with serial tumor samples (primary and relapse) available for 5 of them; somatic variants were identified in 187 AML-related genes, including both novel (SIN3A, C10orf53, PTPRR, and RERGL) and well-known (NPM1, RUNX1, and CEPBA) AMLrelated genes...
May 15, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29760807/quality-control-of-next-generation-sequencing-based-in-vitro-diagnostic-test-for-onco-relevant-mutations-using-multiplex-reference-materials-in-plasma
#6
Donglai Liu, Haiwei Zhou, Dawei Shi, Shu Shen, Yabin Tian, Lin Wang, Jiatao Lou, Rong Cong, Juan Lu, Henghui Zhang, Meiru Zhao, Shida Zhu, Zhisheng Cao, Ruilin Jin, Yin Wang, Xiaoni Zhang, Guohua Yang, Youchun Wang, Chuntao Zhang
Background: Widespread clinical implementation of next-generation sequencing (NGS)-based cancer in vitro diagnostic tests (IVDs) highlighted the urgency to establish reference materials which could provide full control of the process from nucleic acid extraction to test report generation. The formalin-fixed, paraffin-embedded (FFPE) tissue and blood plasma containing circulating tumor deoxyribonucleic acid (ctDNA) were mostly used for clinically detecting onco-relevant mutations. Methods: We respectively developed multiplex FFPE and plasma reference materials covering three clinically onco-relevant mutations within the epidermal growth factor receptor ( EGFR ) gene at serial allelic frequencies...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29758342/next-generation-sequencing-in-drug-development-target-identification-and-genetically-stratified-clinical-trials
#7
REVIEW
Abolfazl Doostparast Torshizi, Kai Wang
Next-generation sequencing (NGS) enabled high-throughput analysis of genotype-phenotype relationships on human populations, ushering in a new era of genetics-informed drug development. The year 2017 was remarkable, with the first FDA-approved gene therapy for cancer (Kymriah™) and for inherited diseases (LUXTURNA™), the first multiplex NGS panel for companion diagnostics (MSK-IMPACT™) and the first drug targeting a genetic signature rather than a disease (Keytruda® ). We envision that population-scale NGS with paired electronic health records (EHRs) will become a routine measure in the drug development process for the identification of novel drug targets, and that genetically stratified clinical trials could be widely adopted to improve power in precision-medicine-guided drug development...
May 11, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29755696/the-use-of-long-non-coding-rnas-as-prognostic-biomarkers-and-therapeutic-targets-in-prostate-cancer
#8
REVIEW
Cristian Arriaga-Canon, Inti Alberto De La Rosa-Velázquez, Rodrigo González-Barrios, Rogelio Montiel-Manríquez, Diego Oliva-Rico, Francisco Jiménez-Trejo, Carlo Cortés-González, Luis A Herrera
Prostate cancer is the most common cancer in men and the second leading cause of cancer-related deaths. The most used biomarker to detect prostate cancer is Prostate Specific Antigen (PSA), whose levels are measured in serum. However, it has been recently established that molecular markers of cancer should not be based solely on genes and proteins but should also reflect other genomic traits; long non-coding RNAs (lncRNAs) serve this purpose. lncRNAs are transcripts of >200 bases that do not encode proteins and that have been shown to display abnormal expression profiles in different types of cancer...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755687/clinical-application-of-targeted-next-generation-sequencing-for-colorectal-cancer-patients-a-multicentric-belgian-experience
#9
Nicky D'Haene, Quitterie Fontanges, Nancy De Nève, Oriane Blanchard, Barbara Melendez, Monique Delos, Marie-Françoise Dehou, Calliope Maris, Nathalie Nagy, Emmanuel Rousseau, Josse Vandenhove, André Gilles, Carine De Prez, Laurine Verset, Marie-Paule Van Craynest, Pieter Demetter, Jean-Luc Van Laethem, Isabelle Salmon, Marie Le Mercier
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755653/tumornext-lynch-mmr-a-comprehensive-next-generation-sequencing-assay-for-the-detection-of-germline-and-somatic-mutations-in-genes-associated-with-mismatch-repair-deficiency-and-lynch-syndrome
#10
Phillip N Gray, Pei Tsai, Daniel Chen, Sitao Wu, Jayne Hoo, Wenbo Mu, Bing Li, Huy Vuong, Hsiao-Mei Lu, Navanjot Batth, Sara Willett, Lisa Uyeda, Swati Shah, Chia-Ling Gau, Monalyn Umali, Carin Espenschied, Mike Janicek, Sandra Brown, David Margileth, Lavinia Dobrea, Lawrence Wagman, Huma Rana, Michael J Hall, Theodora Ross, Jonathan Terdiman, Carey Cullinane, Savita Ries, Ellen Totten, Aaron M Elliott
The current algorithm for Lynch syndrome diagnosis is highly complex with multiple steps which can result in an extended time to diagnosis while depleting precious tumor specimens. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext-Lynch-MMR, which generates a comprehensive genetic profile of both germline and somatic mutations that can accelerate and streamline the time to diagnosis and preserve specimen. TumorNext-Lynch-MMR can detect single nucleotide variants, small insertions and deletions in 39 genes that are frequently mutated in Lynch syndrome and colorectal cancer...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755651/the-clinical-impact-of-using-complex-molecular-profiling-strategies-in-routine-oncology-practice
#11
Jean-François Laes, Philippe Aftimos, Philippe Barthelemy, Joaquim Bellmunt, Guy Berchem, Carlos Camps, Ramón de Las Peñas, Ana Finzel, Jesús García-Foncillas, Petteri Hervonen, Ibrahim Wahid, Timo Joensuu, Louis Kathan, Anthony Kong, James Mackay, Christos Mikropoulos, Kefah Mokbel, Jean-Loup Mouysset, Sergey Odarchenko, Timothy J Perren, Rika Pienaar, Carlos Regonesi, Shadi Salem Alkhayyat, Abdul Rahman El Kinge, Omalkhair Abulkhair, Khaled Morsi Galal, Hady Ghanem, Fadi El Karak, Angel Garcia, Gregori Ghitti, Helen Sadik
Molecular profiling and functional assessment of signalling pathways of advanced solid tumours are becoming increasingly available. However, their clinical utility in guiding patients' treatment remains unknown. Here, we assessed whether molecular profiling helps physicians in therapeutic decision making by analysing the molecular profiles of 1057 advanced cancer patient samples after failing at least one standard of care treatment using a combination of next-generation sequencing (NGS), immunohistochemistry (IHC) and other specific tests...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755432/murine-endogenous-retroviruses-are-detectable-in-patient-derived-xenografts-but-not-in-patient-individual-cell-lines-of-human-colorectal-cancer
#12
Stephanie Bock, Christina S Mullins, Ernst Klar, Philippe Pérot, Claudia Maletzki, Michael Linnebacher
Endogenous retroviruses are remnants of retroviral infections. In contrast to their human counterparts, murine endogenous retroviruses (mERV) still can synthesize infectious particles and retrotranspose. Xenotransplanted human cells have occasionally been described to be mERV infected. With genetic engineered mice and patient-derived xenografts (PDXs) on the rise as eminent research tools, we here systematically investigated, if different tumor models harbor mERV infections. Relevant mERV candidates were first preselected by next generation sequencing (NGS) analysis of spontaneous lymphomas triggered by colorectal cancer (CRC) PDX tissue...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29752822/germline-mutations-in-40-cancer-susceptibility-genes-among-chinese-patients-with-high-hereditary-risk-breast-cancer
#13
Junyan Li, Ruilin Jing, Hongyi Wei, Minghao Wang, Xiaowei Qi, Haoxi Liu, Jian Liu, Jianghua Ou, Weihua Jiang, Fuguo Tian, Yuan Sheng, Hengyu Li, Hong Xu, Ruishan Zhang, Aihua Guan, Ke Liu, Hongchuan Jiang, Yu Ren, Jianjun He, Weiwei Huang, Ning Liao, Xiangjun Cai, Jia Ming, Rui Ling, Yan Xu, Chunyan Hu, Jianguo Zhang, Baoliang Guo, Lizhi Ouyang, Ping Shuai, Zhenzhen Liu, Ling Zhong, Zhen Zeng, Ting Zhang, Zhaoling Xuan, Xuanni Tan, Junbin Liang, Qinwen Pan, Li Chen, Fan Zhang, Linjun Fan, Yi Zhang, Xinhua Yang, Jingbo Li, Chongjian Chen, Jun Jiang
Multigene panel testing of breast cancer predisposition genes have been extensively conducted in Europe and America, which is relatively rare in Asia however. In this study, we assessed the frequency of germline mutations in 40 cancer predisposition genes, including BRCA1 and BRCA2, among a large cohort of Chinese patients with high hereditary risk of BC. From 2015 to 2016, consecutive BC patients from 26 centers of China with high hereditary risk were recruited (n=937). Clinical information was collected and next-generation sequencing (NGS) was performed using blood samples of participants to identify germline mutations...
May 12, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29752549/promising-new-agents-for-colorectal-cancer
#14
REVIEW
Satya Das, Kristen K Ciombor, Sigurdis Haraldsdottir, Richard M Goldberg
Choosing the optimal treatment approach for patients with metastatic colorectal cancer (mCRC) demands that oncologists assess both clinical and genomic variables and individualize care based upon the findings. Clinically, choices depend on assessing the side of the colon in which the primary tumor originates, the sites and burden of metastatic disease, the patient's performance status, and their individual comorbidities. Genomic assessment of the tumor to discern the mutational status of genes such as RAS/RAF, HER2, and TRK, as well as assessing whether tumors have defective mismatch repair (dMMR) or high microsatellite instability (MSI-H), all factor in to potential treatment options and can determine clinical trial eligibility...
May 11, 2018: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/29752127/implementation-of-next-generation-sequencing-technology-for-somatic-mutation-detection-in-routine-laboratory-practice
#15
Tindaro Giardina, Cleo Robinson, Fabienne Grieu-Iacopetta, Michael Millward, Barry Iacopetta, Dominic Spagnolo, Benhur Amanuel
The introduction of next generation sequencing (NGS) in the routine diagnostic setting is still in the development phase and has been limited by its complexity. Targeted NGS offers an attractive alternative to performing multiple single target assays and is very useful in meeting the increasing clinical demand for testing of multiple genetic aberrations in cancer specimens. To this end, we carried out a blinded validation study on 113 tumours in a diagnostic laboratory and compared mutation results from targeted NGS with those from Sanger sequencing, pyrosequencing, competitive allele specific TaqMan polymerase chain reaction (CAST PCR) and Cobas assays...
May 8, 2018: Pathology
https://www.readbyqxmd.com/read/29751042/next-generation-sequencing-analysis-for-gastric-adenocarcinoma-with-enteroblastic-differentiation-emphasis-on-the-relationship-with-hepatoid-adenocarcinoma
#16
Yoichi Akazawa, Tsuyoshi Saito, Takuo Hayashi, Yuka Yanai, Sho Tsuyama, Keisuke Akaike, Yoshiyuki Suehara, Fumiyuki Takahashi, Kazuya Takamochi, Hiroya Ueyama, Takashi Murakami, Sumio Watanabe, Akihito Nagahara, Takashi Yao
Histologically tubulo-papillary structures with glycogen-rich clear cytoplasm in gastric adenocarcinoma with enteroblastic differentiation (GAED) are well-known, but a solid growth pattern can also be observed as a minor component. In contrast, hepatoid adenocarcinoma (HAC) of the stomach shows many overlapping features, including solid pattern and alpha-fetoprotein expression. In this study, we employed next-generation sequencing (NGS) to establish a molecular/clinicopathological concept of GAED and clarify whether these two tumors should be grouped together in one category...
May 8, 2018: Human Pathology
https://www.readbyqxmd.com/read/29740090/next-generation-sequencing-of-urine-exfoliated-cells-an-approach-of-prostate-cancer-micrornas-research
#17
Gabriella Guelfi, Giovanni Cochetti, Valentina Stefanetti, Danilo Zampini, Silvana Diverio, Andrea Boni, Ettore Mearini
There is emerging evidence that microRNAs (miRNAs) dysregulation is involved in the genesis and the progression of Prostate Cancer (PCa), thus potentially increasing their use in urological clinical practice. This is the first pilot study which utilizes Illumina Deep Sequencing to examine the entire miRNAs spectrum existent in urine exfoliated prostate cells (UEPCs) of PCa patients. A total of 11 male patients with histological diagnosis of PCa were enrolled in the present study. First-catch urine (30 mL) was collected following a prostate massage...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29737439/enos-expression-and-no-release-during-hypoxia-is-inhibited-by-mir-200b-in-human-endothelial-cells
#18
Anna Janaszak-Jasiecka, Anna Siekierzycka, Sylwia Bartoszewska, Marcin Serocki, Lawrence W Dobrucki, James F Collawn, Leszek Kalinowski, Rafal Bartoszewski
The nitric oxide (NO) secreted by vascular endothelium is required for the maintenance of cardiovascular homeostasis. Diminished release of NO generated by endothelial NO synthase contributes to endothelial dysfunction. Hypoxia and ischemia reduce endothelial eNOS expression via posttranscriptional mechanisms that result in NOS3 transcript destabilization. Here, we examine whether microRNAs contribute to this mechanism. We followed the kinetics of hypoxia-induced changes in NOS3 mRNA and eNOS protein levels in primary human umbilical vein endothelial cells (HUVECs)...
May 8, 2018: Angiogenesis
https://www.readbyqxmd.com/read/29731958/main-implications-related-to-the-switch-to-brca-1-2-tumor-testing-in-ovarian-cancer-patients-a-proposal-of-a-consensus
#19
Ettore Capoluongo, Giovanni Scambia, Jean-Marc Nabholtz
Background: Since the approval of the first poly (adenosine diphosphate [ADP]) ribose polymerase inhibitor (PARPi; olaparib [Lynparza™]) for platinum-sensitive relapsed high grade ovarian cancer, with either germline or somatic BRCA1/2 deleterious variants, the strategies for BRCA1/2 are dynamically changing. Along with germline testing within the context of familial or sporadic ovarian cancer, patients are now being referred for BRCA1/2 genetic assay above all for treatment decisions: in this setting tumour BRCA assay can allow to identify an estimated 3-9% of patients with peculiar somatic BRCA1/2 mutations...
April 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29726617/copy-number-variant-analysis-using-genome-wide-mate-pair-sequencing
#20
James B Smadbeck, Sarah H Johnson, Stephanie A Smoley, Athanasios Gaitatzes, Travis M Drucker, Roman M Zenka, Farhad Kosari, Stephen J Murphy, Nicole Hoppman, Umut Aypar, William R Sukov, Robert B Jenkins, Hutton M Kearney, Andrew L Feldman, George Vasmatzis
Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable...
May 4, 2018: Genes, Chromosomes & Cancer
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