Search results for " Sequencing"
showing 10 items of 976 documents
Variable presence of 5-methylcytosine in commercial RNA and DNA
2015
Nucleoside methylations and other nucleic acid modifications have recently encountered a surge in interest, prompted, among other things, by the detection of methylation and active demethylation of DNA and mRNA by similar mechanisms. In DNA, deoxycytidine methylation by Dnmt enzymes generates 5-methyldeoxycytidine,1 an important epigenetic mark that typically causes inactivation of transcription of the methylated promoter region. Recent exciting developments have shown that these marks are not concrete-cast, but can be actively removed by the oxidative action of TET enzymes,2 which generate, through a series of 2-electron oxidations, first hydroxymethylcytidine (hm5C), then formyldeoxycytid…
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
2019
Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are…
CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment
2017
Next generation sequencing (NGS) technologies have enabled cheap, large-scale, and high-throughput production of short DNA sequence reads and thereby have promoted the explosive growth of data volume. Unfortunately, the produced reads are short and prone to contain errors that are incurred during sequencing cycles. Both large data volume and sequencing errors have complicated the mapping of NGS reads onto the reference genome and have motivated the development of various aligners for very short reads, typically less than 100 base pairs (bps) in length. As read length continues to increase, propelled by advances in NGS technologies, these longer reads tend to have higher sequencing error rat…
In the literature: February 2019
2019
Malignant pleural mesothelioma (MPM) is a rare and lethal cancer associated to asbestos exposure. Currently, the pemetrexed and cisplatin combination chemotherapy remains the only approved treatment. In the last 5 years, a growing knowledge on mesothelioma pathobiology has translated into the development of multiple novel therapeutic strategies.1 One of the largest reports of comprehensive genomic profiling of MPM was conducted by Bueno and colleagues. Using RNA-seq data, they identified four distinct molecular subtypes, and through exome analysis, they found that BAP1 , NF2 , TP53 , SETD2 , DDX3X , ULK2 , RYR2 , CFAP45 , SETDB1 and DDX51 were significantly mutated.2 In an article recently …
Why do results conflict regarding the prognostic value of the methylation status in colon cancers? The role of the preservation method.
2012
Abstract Background In colorectal carcinoma, extensive gene promoter hypermethylation is called the CpG island methylator phenotype (CIMP). Explaining why studies on CIMP and survival yield conflicting results is essential. Most experiments to measure DNA methylation rely on the sodium bisulfite conversion of unmethylated cytosines into uracils. No study has evaluated the performance of bisulfite conversion and methylation levels from matched cryo-preserved and Formalin-Fixed Paraffin Embedded (FFPE) samples using pyrosequencing. Methods Couples of matched cryo-preserved and FFPE samples from 40 colon adenocarcinomas were analyzed. Rates of bisulfite conversion and levels of methylation of …
Application of patient-derived liver cancer cells for phenotypic characterization and therapeutic target identification.
2018
Primary liver cancer (PLC) ranks among the most lethal solid cancers worldwide due to lack of effective biomarkers for early detection and limited treatment options in advanced stages. Development of primary culture models that closely recapitulate phenotypic and molecular diversities of PLC is urgently needed to improve the patient outcome. Long-term cultures of 7 primary liver cancer cell lines of hepatocellular and cholangiocellular origin were established using defined culture conditions. Morphological and histological characteristics of obtained cell lines and xenograft tumors were analyzed and compared to original tumors. Time course analyses of transcriptomic and genomic changes were…
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
2015
Abstract Analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed regional DNA hypermethylation embedded in extensive global hypomethylation. In contrast to the widely reported DNA hypermethylation of promoter-associated CpG islands (CGIs) in cancer, hypermethylated sites in MM as compared to normal plasma cells were located outside CpG islands and were unexpectedly associated with intronic enhancer regions active in normal B cells. Both RNA-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with downregulation of its host genes. ChIP-seq and DNAseI-se…
Germline Predisposition to Pediatric Cancer, from Next Generation Sequencing to Medical Care
2021
Knowledge about genetic predisposition to pediatric cancer is constantly expanding. The categorization and clinical management of the best-known syndromes has been refined over the years. Meanwhile, new genes for pediatric cancer susceptibility are discovered every year. Our current work shares the results of genetically studying the germline of 170 pediatric patients diagnosed with cancer. Patients were prospectively recruited and studied using a custom panel, OncoNano V2. The well-categorized predisposing syndromes incidence was 9.4%. Likely pathogenic variants for predisposition to the patient’s tumor were identified in an additional 5.9% of cases. Additionally, a high number of pathogen…
Molecular aspects of carcinogenesis. Part B
1989
Nitrogen mustards represent a major group of alkylating agents that are used in the chemotherapy of cancer. It is commonly accepted that they exert their cytotoxic effects by their ability to produce interstrand crosslinks in DNA. The main target site of the two identical alkylating moieties is the N-7 position of guanine. By a Maxam-Gilbert-type reaction it is possible to identify "hot spots" for alkylation by nitrogen mustards. Analysis of data obtained reveal the importance of the DNA context for efficient alkylation. For most of~ the compounds the highest reactivity is observed ila regions of G clusters, while in the neighbourhood of cytosine residues alkylation is reduced. As a consequ…
Liver Transplantation for Unresectable Intrahepatic Cholangiocarcinoma: The Role of Sequencing Genetic Profiling
2021
Simple Summary Intrahepatic cholangiocarcinoma is a rare disease with increasing incidence and mortality still characterized by an insufficient clinical outcome. Growing attention has recently surrounded this disease, and liver transplantation has emerged as a novel curative treatment for cholangiocarcinoma, along with a better understanding of genetic alterations potentially capable of driving tumorigenesis. The aim of this paper is to present a clinical description of our case series of patients affected by intrahepatic cholangiocarcinoma and by mixed forms of hepatocellular and cholangiocellular carcinoma, together with a genomic profiling of mutations occurring in a panel of genes relev…