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https://www.readbyqxmd.com/read/28717669/pitfalls-in-genetic-testing-a-case-of-a-snp-in-primer-annealing-region-leading-to-allele-dropout-in-brca1
#1
Felipe Carneiro Silva, Giovana Tardin Torrezan, Rafael Canfield Brianese, Raquel Stabellini, Dirce Maria Carraro
BACKGROUND: Hereditary breast and ovarian cancer is characterized by mutations in BRCA1 or BRCA2 genes and PCR-based screening techniques, such as capillary sequencing and next-generation sequencing (NGS), are considered gold standard methods for detection of pathogenic mutations in these genes. Single-nucleotide polymorphisms (SNPs) constitute a vast source of variation in the human genome and represent a risk for misdiagnosis in genetic testing, since the presence of a SNP in primer-annealing sites may cause false negative results due to allele dropout...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717660/a-novel-molecular-diagnostics-platform-for-somatic-and-germline-precision-oncology
#2
Rubén Cabanillas, Marta Diñeiro, David Castillo, Patricia C Pruneda, Cristina Penas, Guadalupe A Cifuentes, Álvaro de Vicente, Noelia S Durán, Rebeca Álvarez, Gonzalo R Ordóñez, Juan Cadiñanos
BACKGROUND: Next-generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28716721/the-evolving-genomic-landscape-of-barrett-s-esophagus-and-esophageal-adenocarcinoma
#3
REVIEW
Gianmarco Contino, Thomas L Vaughan, David Whiteman, Rebecca Fitzgerald
We have recently gained unprecedented insight into genetic factors that determine risk for Barrett's esophagus (BE) and progression to esophageal adenocarcinoma (EA). Next-generation sequencing technologies have allowed us to identify somatic mutations that initiate BE and track genetic changes during development of tumors and invasive cancer. These technologies led to identification of mechanisms of tumorigenesis that challenge the current multi-step model of progression to EA. Newer, cost-effective technologies create opportunities to rapidly translate the analysis of DNA into tools that can identify patients with BE at high risk for cancer, detect dysplastic lesions at earlier stages, and uncover mechanisms of carcinogenesis...
July 14, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28716111/quantitation-of-dna-methylation-in-epstein-barr-virus-associated-nasopharyngeal-carcinoma-by-bisulfite-amplicon-sequencing
#4
Weilin Zhao, Yingxi Mo, Shumin Wang, Kaoru Midorikawa, Ning Ma, Yusuke Hiraku, Shinji Oikawa, Guangwu Huang, Zhe Zhang, Mariko Murata, Kazuhiko Takeuchi
BACKGROUND: Epigenetic changes, including DNA methylation, disrupt normal cell function, thus contributing to multiple steps of carcinogenesis. Nasopharyngeal carcinoma (NPC) is endemic in southern China and is highly associated with Epstein-Barr virus (EBV) infection. Significant changes of the host cell methylome are observed in EBV-associated NPC with cancer development. Epigenetic marks for NPC diagnosis are urgently needed. In order to explore DNA methylation marks, we investigated DNA methylation of candidate genes in EBV-associated nasopharyngeal carcinoma...
July 17, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28713573/a-monograph-proposing-the-use-of-canine-mammary-tumours-as-a-model-for-the-study-of-hereditary-breast-cancer-susceptibility-genes-in-humans
#5
REVIEW
Katie Goebel, Nancy D Merner
Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra-breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour...
May 2017: Veterinary Medicine and Science
https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#6
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28712319/primary-liver-cancer-genome-sequencing-translational-implications-and-challenges
#7
Demosthenes E Ziogas, Ioannis D Kyrochristos, Georgios K Glantzounis, Dimitrios Christodoulou, Evangelos Felekouras, Dimitrios H Roukos
The prognosis of primary liver cancer (PLC) remains poor and is explained by the slow progress in understanding the molecular pathways driving tumorigenesis, therapeutic resistance and relapse. For early PLCs, complete surgical resection is the only effective treatment, with sorafenib and, more recently, regorafenib prolonging overall survival by a few months. Areas covered: Application of next-generation sequencing (NGS), including targeted NGS (tNGS), whole-exome sequencing (WES), whole-genome sequencing (WGS) and RNA sequencing (RNAseq), on clinical samples from patients with hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) could aid in comprehending tumorigenesis, genetic and genomic heterogeneity, as well as developing molecular classifications for specialized targeted therapy...
July 17, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28710706/synchronous-and-metastatic-papillary-and-follicular-thyroid-carcinomas-with-unique-molecular-signatures
#8
Vincent Cracolici, Ibro Mujacic, Sabah Kadri, Mir Alikhan, Nifang Niu, Jeremy P Segal, Lauren E Rosen, David H Sarne, Adam Morgan, Samy Desouky, Nicole A Cipriani
Despite the relatively high prevalence of thyroid cancer, the occurrence of multiple synchronous, distinct subtypes of primary thyroid carcinoma is uncommon. The incidental finding of papillary thyroid microcarcinoma in a gland with a biologically relevant follicular or medullary carcinoma is more frequent than the synchronous occurrence of multiple clinically significant carcinomas. We report a case of synchronous papillary and follicular thyroid carcinomas metastatic to lymph node and bone, respectively. Next generation sequencing showed BRAF V600E mutation in the primary papillary carcinoma and NRAS Q61R mutation in the primary follicular carcinoma and bony metastasis...
July 14, 2017: Endocrine Pathology
https://www.readbyqxmd.com/read/28708103/pharmacogenomics-of-targeted-agents-for-personalization-of-colorectal-cancer-treatment
#9
REVIEW
Alessia Bignucolo, Elena De Mattia, Erika Cecchin, Rossana Roncato, Giuseppe Toffoli
The use of targeted agents in the treatment of metastatic colorectal cancer (CRC) has improved patient outcomes. Anti-epidermal growth factor receptor (anti-EGFR) agents (cetuximab and panitumumab) and antiangiogenic molecules (bevacizumab, regorafeninb, ramucirumab, and aflibercept) have been successfully integrated into clinical practice. Other drugs have been designed to target additional deregulated pathways in CRC, such as MAPK (mitogen-activated protein kinase)/PI3K-AKT (phosphatidylinositol-3-kinase-AKT serine/threonine kinase)/mTOR (mammalian target of rapamycin), HER-2 and 3 ( human epidermal growth factor receptor-2 and -3), and BRAF...
July 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28706762/metastatic-breast-cancer-with-brca-mutation-discovered-by-next-generation-sequencing-responding-to-olaparib
#10
Wajeeha Rizvi, Phu Truong, Quoc Truong
Breast cancer susceptibility genes 1 and 2 (BRCA1 and BRCA2) mutations are associated with hereditary breast and ovarian cancer syndromes (HBOC). However, certain individuals with breast cancer do not meet high-risk factors for hereditary breast cancer screening based on age, family history, and biology of malignancy. We present a patient with relapsed breast cancer who developed progressive disease with significant tumor burden causing a recurrent pleural effusion. Next-generation sequencing (NGS) done on a tumor biopsy was positive for the BRCA2 mutation...
June 11, 2017: Curēus
https://www.readbyqxmd.com/read/28706143/integrated-analysis-of-somatic-mutations-and-immune-microenvironment-of-multiple-regions-in-breast-cancers
#11
Taigo Kato, Jae-Hyun Park, Kazuma Kiyotani, Yuji Ikeda, Yasuo Miyoshi, Yusuke Nakamura
Next-generation sequencing technology enables us to analyze the complexity of intra- and inter-tumoral heterogeneity, which may influence to prognosis of cancer patients. In this study, we collected surgically-resected tumor tissues from five breast cancer patients and characterized three different portions of individual tumors through somatic mutation analysis by whole exome sequencing, T cell receptor beta (TCRB) repertoire analysis of tumor-infiltrating lymphocytes (TILs), and the expression analysis of immune-related genes at 15 different sites...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28704519/e2f1-somatic-mutation-within-mirna-target-site-impairs-gene-regulation-in-colorectal-cancer
#12
Camila M Lopes-Ramos, Bruna P Barros, Fernanda C Koyama, Paola A Carpinetti, Julia Pezuk, Nayara T S Doimo, Angelita Habr-Gama, Rodrigo O Perez, Raphael B Parmigiani
BACKGROUND: Genetic studies have largely concentrated on the impact of somatic mutations found in coding regions, and have neglected mutations outside of these. However, 3' untranslated regions (3' UTR) mutations can also disrupt or create miRNA target sites, and trigger oncogene activation or tumor suppressor inactivation. METHODS: We used next-generation sequencing to widely screen for genetic alterations within predicted miRNA target sites of oncogenes associated with colorectal cancer, and evaluated the functional impact of a new somatic mutation...
2017: PloS One
https://www.readbyqxmd.com/read/28698198/abcb1-mediates-cabazitaxel-docetaxel-cross-resistance-in-advanced-prostate-cancer
#13
Alan P Lombard, Chengfei Liu, Cameron M Armstrong, Vito Cucchiara, Xinwei Gu, Wei Lou, Christopher P Evans, Allen C Gao
in research have added several new therapies for castration-resistant prostate cancer (CRPC), greatly augmenting our ability to treat patients. However, CRPC remains an incurable disease due to the development of therapeutic resistance and the existence of cross-resistance between available therapies. Understanding the interplay between different treatments will lead to improved sequencing and the creation of combinations which overcome resistance and prolong survival. Whether there exists cross-resistance between docetaxel and the next-generation taxane cabazitaxel is poorly understood...
July 11, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28696559/genetic-testing-for-hereditary-nonpolyposis-colorectal-cancer-hnpcc
#14
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary nonpolyposis colorectal cancer (HNPCC), also called Lynch syndrome, is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. Lynch syndrome accounts for up to 3% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28695659/epstein-barr-virus-negative-extranodal-true-natural-killer-cell-lymphoma-harbouring-a-kdm6a-mutation
#15
Naoko Tsuyama, Reimi Asaka, Akito Dobashi, Satoko Baba, Yuko Mishima, Kyoko Ueda, Masahiko Oguchi, Hideki Tsuji, Kiyohiko Hatake, Kengo Takeuchi
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (ENKTL) is an extranodal aggressive T or NK-cell lymphoma that is characteristically associated with Epstein-Barr virus (EBV) infection and cytotoxic tissue-destructive features. Although ENKTL is described as a distinct entity according to the 2008 WHO classification, a considerable complexity is associated with the differential diagnosis of other T-cell lymphomas with respect to tumour cell origins, locations, and the presence of EBV infection, as well as molecular and cytogenetic abnormalities...
July 10, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/28693246/genetic-alterations-in-japanese-extrahepatic-biliary-tract-cancer
#16
Rei Noguchi, Kiyoshi Yamaguchi, Tsuneo Ikenoue, Yumi Terakado, Yasunori Ohta, Naohide Yamashita, Osamu Kainuma, Sana Yokoi, Yoshiaki Maru, Hiroki Nagase, Yoichi Furukawa
Biliary tract cancer (BTC) is one of the most devastating types of malignant neoplasms worldwide. However, the mechanisms underlying the development and progression of BTC remain unresolved. BTC includes extrahepatic bile duct carcinoma (EBDC), gallbladder carcinoma (GBC) and ampulla of Vater carcinoma (AVC), named according to the location of the tumor. Although genetic alterations of intrahepatic cholangiocarcinoma have been investigated, those of EBDC, GBC and AVC have not yet been fully understood. The present study analyzed somatic mutations of 50 cancer-associated genes in 27 Japanese BTC cells, including: 11 EBDC, 14 GBC and 2 AVC...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28693210/resistance-to-epithelial-growth-factor-receptor-tyrosine-kinase-inhibitors-in-a-patient-with-transformation-from-lung-adenocarcinoma-to-small-cell-lung-cancer-a-case-report
#17
Liying Fang, Jian He, Jingwen Xia, Liang Dong, Xiujuan Zhang, Yaqin Chai, Ying Li, Mengjie Niu, Tianxing Hang, Shengqing Li
First-generation epithelial growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have markedly improved the treatment of non-small cell lung cancer (non-SCLC) with EGFR-sensitive mutations. However, acquired resistance to these drugs was inevitable. The transformation of lung adenocarcinoma to SCLC following treatment with EGFR-TKIs is a rare phenomenon that contributes to resistance to EGFR-TKIs. The present case concerns a 74-year-old man previously diagnosed with and treated for pneumonia; however, this was later pathologically confirmed as lung adenocarcinoma by transbronchial lung biopsy...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28693197/recent-developments-in-predictive-biomarkers-of-pediatric-glioma
#18
Zhengwei Li, Yiyu Yin, Fengli Liu
The presence of certain cancer-related genetic and epigenetic alterations in the tumor affects patient response to specific cancer therapies. The accurate screening of these predictive biomarkers in molecular diagnostics is important since it enables the tailoring of optimal treatment based on molecular characteristics of the tumor. We searched the electronic database PubMed for preclinical as well as clinical controlled trials reporting on various multiple predictors of glioma. It was observed clearly that multiple approaches are evolving and a few of them have also shown promising results...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28693166/quantitative-analysis-and-clonal-characterization-of-t-cell-receptor-%C3%AE-repertoires-in-patients-with-advanced-non-small-cell-lung-cancer-treated-with-cancer-vaccine
#19
Tu Mai, Atsushi Takano, Hiroyuki Suzuki, Takashi Hirose, Takahiro Mori, Koji Teramoto, Kazuma Kiyotani, Yusuke Nakamura, Yataro Daigo
With the development of cancer immunotherapy that may activate T cells, a practical and quantitative method to improve monitoring and/or prediction of immunological response of patients as a predictive biomarker is of importance. To examine possible biomarkers for a therapeutic cancer vaccine containing a mixture of three epitope peptides derived from cell division-associated 1, lymphocyte antigen 6 complex locus K and insulin-like growth factor-II mRNA-binding protein 3, T-cell receptor β (TCRβ) repertoires of blood samples from 24 patients with human leukocyte antigen-A*2402-positive non-small cell lung cancer were characterized prior to and following 8 weeks of the cancer vaccine treatment, by applying a next-generation sequencing method...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28691344/combined-tumor-genomic-profiling-and-exome-sequencing-in-a-breast-cancer-family-implicates-atm-in-tumorigenesis-a-proof-of-principle-study
#20
Virginie Bubien, Françoise Bonnet, Jennifer Dupiot-Chiron, Emmanuelle Barouk-Simonet, Natalie Jones, Aurélien de Reynies, Gaëtan MacGrogan, Nicolas Sevenet, Eric Letouzé, Michel Longy
Familial breast cancers (BCs) account for 10-20% of all diagnosed BCs, yet only 20% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes non BRCA1 and non BRCA2 (or BRCAx) families makes grouped studies impossible to perform. Next generation sequencing techniques, however, allow individual families to be studied in order to identify rare and or private mutations but the high number of genetic variants identified need to be sorted using pathogenicity or recurrence criteria...
July 10, 2017: Genes, Chromosomes & Cancer
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