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Cancer Next Generation Sequencing

Lingfang Feng, Jianlin Lou
DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal biology and diseases including cancer...
2019: Methods in Molecular Biology
Nobuyuki Bandoh, Toshiaki Akahane, Takashi Goto, Michihisa Kono, Haruyuki Ichikawa, Takahiro Sawada, Tomomi Yamaguchi, Hiroshi Nakano, Yumiko Kawase, Yasutaka Kato, Hajime Kamada, Yasuaki Harabuchi, Kazuo Shimizu, Hiroshi Nishihara
Thyroid carcinoma (TC) has characteristic genetic alterations, including point mutations in proto-oncogenes and chromosomal rearrangements that vary by histologic subtype. Recent developments in next-generation sequencing (NGS) technology enable simultaneous analysis of cancer-associated genes of interest, thus improving diagnostic accuracy and allowing precise personalized treatment for human cancer. A total of 50 patients who underwent thyroidectomy between 2014 and 2016 at Hokuto Hospital were enrolled. Total DNA was extracted from formalin-fixed, paraffin-embedded tissue sections and quantified...
December 2018: Oncology Letters
Ching-Hon Pui, Kim E Nichols, Jun J Yang
Advances in genomic research and risk-directed therapy have led to improvements in the long-term survival and quality of life outcomes of patients with childhood acute lymphoblastic leukaemia (ALL). The application of next-generation sequencing technologies, especially transcriptome sequencing, has resulted in the identification of novel molecular subtypes of ALL with prognostic and therapeutic implications, as well as cooperative mutations that account for much of the heterogeneity in clinical responses observed among patients with specific ALL subtypes...
December 13, 2018: Nature Reviews. Clinical Oncology
Ivana Kašubová, Veronika Holubeková, Katarína Janíková, Barbora Váňová, Zuzana Sňahničanová, Michal Kalman, Lukáš Plank, Zora Lasabová
The development of the new technologies such as the next-generation sequencing (NGS) makes more accessible the diagnosis of genetically heterogeneous diseases such as Lynch syndrome (LS). LS is one of the most common hereditary form of colorectal cancer. This autosomal dominant inherited disorder is caused by deleterious germline mutations in one of the mismatch repair (MMR) genes - MLH1, MSH2, MSH6 or PMS2, or the deletion in the EPCAM gene. These mutations eventually result in microsatellite instability (MSI), which can be easily tested in tumor tissue...
2018: Acta Medica (Hradec Králové)
Shu-Hsuan Liu, Wei-Chung Cheng
Next generation sequencing (NGS) has become the norm of cancer genomic researches. Large-scale cancer sequencing projects seek to comprehensively uncover mutated genes that confer a selective advantage for cancer cells. Numerous computational algorithms have been developed to find genes that drive cancer based on their patterns of mutation in a patient cohort. It has been noted that the distinct features of driver gene alterations in different subgroups are based on clinical characteristics. Previously, we have developed a database, DriverDB, to integrate all public cancer sequencing data and to identify cancer driver genes according to bioinformatics tools...
2019: Methods in Molecular Biology
Shiho Takeuchi, Shujiro Okuda
In Japan, the National Cancer Center and university hospitals have initiated next-generation sequencing-based in vitro diagnostic testing for cancer patients as a method of clinical sequencing. Based on the molecular alterations detected, physicians can provide approved targeted therapy and access to investigational drugs for cancer patients. However, interpretation of the clinical significance of genomic alterations remains the most severe bottleneck of precision medicine in cancer. Although many research institutes in the United States are developing knowledge bases for interpretation of the tumor alterations and clinical decisions, these knowledge bases are unsuited as sources of reference in Japan due to differences in the information on approved drugs and implementation of clinical trials...
December 12, 2018: International Journal of Clinical Oncology
Chia-Yi Hsu, Tsung-Hua Hsieh, Tze-Kiong Er, Hung-Sheng Chen, Ching-Chou Tsai, Eing-Mei Tsai
Ovarian cancer is the one of the most lethal gynecological cancer types. MicroRNAs (miRs) are noncoding RNAs that modulate the translation of their target mRNAs via binding to a complementary sequence in the target 3' untranslated region, and the dysregulation of certain miRs has been demonstrated to contribute to cancer progression. In this regard, the current study extended our previous work and used next‑generation sequencing data to search for upstream regulators of genetic alterations that are common in ovarian cancer, as well as the miRs that are involved in controlling the expression of these regulators...
October 9, 2018: Oncology Reports
Shingo Kato, Takuo Hayashi, Yoshiyuki Suehara, Haruka Hamanoue, Shoji Yamanaka, Yasushi Ichikawa, Takuma Higurashi, Kenichi Ohashi, Shigeo Yamaguchi, Yumi Nozaki, Yasuhisa Terao, Tsuyoshi Saito
Background: Application of next-generation DNA sequencing (NGS) has recently become increasingly common in the field of clinical oncology in several countries around the world. In Japan also, a system for applying NGS to routine clinical practice is gradually being established. During this process, we introduced in Japan the tumor-profiling MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) assay. Methods: We present here our initial experience with the use of MSK-IMPACT in 68 patients selected from two institutions in Japan between June 2016 and October 2017...
December 12, 2018: Japanese Journal of Clinical Oncology
An-Shun Tai, Chien-Hua Peng, Shih-Chi Peng, Wen-Ping Hsieh
Multistage tumorigenesis is a dynamic process characterized by the accumulation of mutations. Thus, a tumor mass is composed of genetically divergent cell subclones. With the advancement of next-generation sequencing (NGS), mathematical models have been recently developed to decompose tumor subclonal architecture from a collective genome sequencing data. Most of the methods focused on single-nucleotide variants (SNVs). However, somatic copy number aberrations (CNAs) also play critical roles in carcinogenesis...
2018: PloS One
Valerie A Arboleda, Rena R Xian
The development of rapid parallel sequencing in the last 20 years has begun a revolution in the field of genetics that is changing nearly all disciplines within biology and medicine. Genomic sequencing has become crucial to the diagnosis and clinical management of patients with constitutional diseases and cancer and has quickly become an integral part of the new era of personalized and precision medicine. The precision medicine initiative, released by the NIH in 2015, has catapulted genomic technologies to the forefront of the practice of medicine and biomedical research...
2019: Methods in Molecular Biology
Yanni Zhang, Huishuang Chen, Zhiyu Peng, Santasree Banerjee, Wei Li, Zhaolong Zhao, Jianbin Sun, Jian Lv, Hui Huang, Ru Bai, Keke Lin, Zhongxin Li
Lynch syndrome is a genetically and clinically heterogeneous disorder; it is caused by a germline mutation in DNA mismatch repair (MMR) genes. Individuals with a heterozygous mutation in MLH1 have an increased risk for developing colorectal cancer. Here we described a 5-generation Chinese Lynch syndrome family with different severity and onset age. A novel heterozygous germline mutation (c.3G>T, p.Met1Ile) in MLH1 gene was discovered by next generation sequencing. Our study also revealed by qPCR that the MLH1 mRNA expression in peripheral blood of patients in this family was remarkably lower than that of the unaffected carriers and non-carriers...
2018: BioMed Research International
Yubo Fan, Yifan Meng, Shuo Yang, Ling Wang, Wenhua Zhi, Cordelle Lazare, Canhui Cao, Peng Wu
Cervical cancer is the second leading cause of death in female genital malignancies. Persistent infection with high-risk HPV is closely related to cervical intraepithelial neoplasia (CIN). Wide-scale HPV screening has already been implemented in developed countries. However, with advances in HPV testing methods, there are presently no better methods for the management of the increasing number of high-risk HPV-positive women except for periodic review. In order to improve screening coverage and achieve better triage of those women, we present current HPV testing methods with self-collected cervical samples, focusing on recent advances in next-generation sequencing (NGS) technologies as a promising screening technology for cervical cancer precursors...
2018: Disease Markers
Jing Zhai, Gabriel Giannini, Mark D Ewalt, Elizabeth Y Zhang, Marta Invernizzi, Joyce Niland, Lily L Lai
Metaplastic breast carcinoma (MBC) is a rare subtype of breast cancer with variable morphology. MBC is more often triple negative (ER-, PR-, HER2-) and is associated with poorer clinical outcome when compared to infiltrating ductal carcinoma. The purpose of our study is to identify molecular alterations in MBC using next generation sequencing (NGS) which may aid chemotherapy selection and use of targeted therapy. A cohort of 18 patients with MBC yielded adequate DNA from microdissected formalin fixed and paraffin embedded (FFPE) tumor blocks...
December 8, 2018: Human Pathology
J H Francis, T Milman, H Grossniklaus, D M Albert, R Folberg, G M Levitin, S E Coupland, F Catalanotti, D Rabady, C Kandoth, K J Busam, D H Abramson
PURPOSE: GNAQ mutations have been identified in port wine stains (both syndromic and non-syndromic) and melanocytic ocular neoplasms. This study investigates the presence of GNAQ mutations in diffuse- (those associated with Sturge-Weber syndrome (SWS)) and solitary choroidal hemangiomas. PARTICIPANTS: Tissue from 11 patients with the following diagnoses: port wine stain (n = 3), diffuse choroidal hemangioma (n = 1), solitary choroidal hemangioma (n = 6), choroidal nevus (n =1) METHODS: Ten specimens were interrogated with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 468 key cancer genes in formalin-fixed, paraffin-embedded tumors...
December 8, 2018: Ophthalmology
Shib Sankar Bhowmick, Debotosh Bhattacharjee, Luis Rato
BACKGROUND: Identification of differentially expressed genes, i.e., genes whose transcript abundance level differs across different biological or physiological conditions, was indeed a challenging task. However, the inception of transcriptome sequencing (RNA-seq) technology revolutionized the simultaneous measurement of the transcript abundance levels for thousands of genes. OBJECTIVE: In this paper, such next-generation sequencing (NGS) data is used to identify biomarker signatures for several of the most common cancer types (bladder, colon, kidney, brain, liver, lung, prostate, skin, and thyroid) METHODS: Here, the problem is mapped into the comparison of optimization algorithms for selecting a set of genes that lead to the highest classification accuracy of a two-class classification task between healthy and tumor samples...
December 8, 2018: Genes & Genomics
Ildikó Huliák, László Bodai, Mátyás Czepán, Dávid Kovács, Anikó Szabó, László Tiszlavicz, György Lázár, Zoltán Rakonczay, Péter Hegyi, Imre Miklós Boros, Mónika Kiricsi
Myofibroblasts (MFs) are present in healthy tissues and are also key components of the tumor microenvironment. In the present study a comparative analysis of MFs obtained from various gastrointestinal tumor tissues and from tumor‑adjacent normal tissues of cancer patients was performed, with the aim to evaluate differences in MF morphology, gene expression profile and function. The goal was to correlate the observed morphological and functional variations with the underlying genetic and epigenetic backgrounds...
December 6, 2018: Oncology Reports
J Zugazagoitia, I Ramos, J M Trigo, M Palka, A Gómez-Rueda, E Jantus-Lewintre, C Camps, D Isla, P Iranzo, S Ponce-Aix, R García-Campelo, M Provencio, F Franco, R Bernabé, O Juan-Vidal, E Felip, J de Castro, J M Sanchez-Torres, I Faul, R B Lanman, P Garrido, L Paz-Ares
Introduction: Approximately 30% of tumor biopsies from patients with advanced-stage lung adenocarcinomas yield insufficient tissue for successful molecular subtyping. We have analyzed the clinical utility of next-generation sequencing (NGS) of cell-free circulating tumor DNA (ctDNA) in patients with inadequate tumor samples for tissue genotyping. Methods: We conducted the study in a multi-institutional prospective cohort of clinically unselected patients with advanced-stage lung adenocarcinomas with insufficient tissue for EGFR, ALK or ROS1 genotyping across 12 Spanish institutions (n = 93)...
December 10, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Sunil Kumar, Daniel Lindsay, Q Brent Chen, Amy L Garrett, Xianming M Tan, Carey K Anders, Lisa A Carey, Gaorav P Gupta
Serial monitoring of plasma DNA mutations in estrogen receptor positive metastatic breast cancer (ER + MBC) holds promise as an early predictor of therapeutic response. Here, we developed dPCR-SEQ, a customized assay that utilizes digital PCR-based target enrichment followed by next-generation sequencing to analyze plasma DNA mutations in ESR1 , PIK3CA , and TP53 . We validated dPCR-SEQ in a prospective cohort of 58 patients with ER + MBC and demonstrate excellent concordance with hotspot ESR1 mutation abundance measured by conventional digital PCR...
2018: NPJ Breast Cancer
Francesca Arruga, Tiziana Vaisitti, Silvia Deaglio
The systematic application of next-generation sequencing to large cohorts of oncologic samples has opened a Pandora's box full of known and novel genetic lesions implicated in different steps of cancer development and progression. Narrowing down to B cell malignancies, many previously unrecognized genes emerged as recurrently mutated. The challenge now is to determine how the mutation in a given gene affects the biology of the disease, paving the way to functional genomics studies. Mutations in NOTCH family members are shared by several disorders of the B series, even if with variable frequencies and mutational patterns...
2018: Frontiers in Oncology
Omar Hasan Ali, Fiamma Berner, David Bomze, Mirjam Fässler, Stefan Diem, Antonio Cozzio, Markus Jörger, Martin Früh, Christoph Driessen, Tobias L Lenz, Lukas Flatz
BACKGROUND: Checkpoint inhibitors (CIs) are highly effective but can induce severe immune-related adverse events (irAEs), which cannot be predicted. We investigated whether human leukocyte antigen (HLA) genes predispose to developing of irAEs during therapy and thus hold a predictive role. METHODS: We established a prospective observational single-centre study and collected data from patients with either metastatic non-small cell lung cancer (NSCLC) or metastatic melanoma, who were treated with anti-PD-1 (programmed cell death receptor 1), anti-CTLA4 (cytotoxic T-lymphocyte-associated protein 4) or both CIs combined...
December 6, 2018: European Journal of Cancer
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