China
Africa
Explore chapters and articles related to this topic
RNA-seq Analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
With the advent of the second-generation (a.k.a next-generation or high-throughput) sequencing technologies, the number of genes that can be profiled for expression levels with a single experiment has increased to the order of tens of thousands of genes. Therefore, the bottleneck in this process has become the data analysis rather than the data generation. Many statistical methods and computational tools are required for getting meaningful results from the data, which comes with a lot of valuable information along with a lot of sources of noise. Fortunately, most of the steps of RNA-seq analysis have become quite mature over the years. Below we will first describe how to reach a read count table from raw fastq reads obtained from an Illumina sequencing run. We will then demonstrate in R how to process the count table, make a case-control differential expression analysis, and do some downstream functional enrichment analysis.
Comparative Genomic Hybridization and Copy Number Abnormalities in Breast Cancer
Published in Brian Leyland-Jones, Pharmacogenetics of Breast Cancer, 2020
Array CGH technologies are becoming increasingly powerful tools for the identification of recurrent genome CNAs that are associated with outcome or response to therapy in breast and other cancers (63). The ability to detect genetic copy number changes of both large and small scales will be critical in evaluating the most effective therapies on an individual patient basis. In the short term, array CGH will likely be accomplished using commercial oligonucleotide analysis platforms that allow assessment of allele-specific copy number using material from FFPE samples. In the long term, however, array CGH may be supplanted by high-throughput sequencing technologies that allow assessment of both copy number and DNA sequence through deep sequencing. It is already clear that shotgun sequencing, if done at sufficient redundancy, offers the same or better resolution than CGH platforms (64,65). Next-generation sequencing platforms based on massively parallel single-molecule sequencing promise sufficiently low-cost sequencing, so that these platforms may become a viable alternative to array CGH (66,67). Today, this is not cost effective, but costs of high-throughput sequencing are falling rapidly, so these approaches should be followed closely.
Whole exome and whole genome sequencing
Published in Moshe Hod, Vincenzo Berghella, Mary E. D'Alton, Gian Carlo Di Renzo, Eduard Gratacós, Vassilios Fanos, New Technologies and Perinatal Medicine, 2019
In next-generation genomic sequencing, the DNA is cut into small fragments of approximately 1,000–10,000 base pairs (bp); 50–250 bp from each end of the fragment are the “read.” Each read is paired with the read from the opposite end of the fragment; these are termed “paired-end” reads. The pool of fragments is called the “sequencing library.” With WGS, the entire genome is sequenced, while with ES, only the 1%–2% of the genes that include the coding exons are sequenced. With ES, the DNA fragments that overlap with exons and their flanking introns are purified from the entire library. A similar methodology is used for high-throughput sequencing with disease-specific multigene panels.
Gastric protective effect of Alpinia officinarum flavonoids: mediating TLR4/NF-κB and TRPV1 signalling pathways and gastric mucosal healing
Published in Pharmaceutical Biology, 2023
Kaiwen Lin, Tang Deng, Huijuan Qu, Hongya Ou, Qifeng Huang, Bingmiao Gao, Xiaoliang Li, Na Wei
High-throughput sequencing is a transcriptome sequencing technique. Through sample preparation, library establishment, mRNA sequencing operation and data screening and analysis, the mechanism of candidate genes or potential molecular signal pathways are identified (Hrdlickova et al. 2017; Yang et al. 2020). According to GO enrichment analysis (Figure 5(B)), we speculated that F.AOH might improve or inhibit GU occurrence by enriching and regulating immune response, participating in the oxidative stress process, protecting the integrity of gastric mucosa, and regulating cell adhesion. Furthermore, based on KEGG pathway enrichment analysis results (Figure 5(D)), we speculated that F.AOH could improve the immune function of rats, control metabolic disorders, enhance the information transmission of biological cascade reactions, regulate cell proliferation, migration, apoptosis, protect the integrity of gastric mucosa, and prevent GU from developing to severe or even canceration. Then, Toll-like receptors signalling pathways, regulation of inflammatory mediators TRP channels, and PI3K-Akt signalling pathway in several key genes and proteins for validation were chosen. Finally, we found FAOH treatment can promote GU anti-inflammatory analgesic action, promote healing of ulcers of tissue repair, and epithelial cell proliferation and migration to improve the cure rate of GU. The pathological mechanism of these imbalances is closely related to GU occurrence and development (Tarnawski and Ahluwalia 2012).
Diversity in matrilineages among the Jomon individuals of Japan
Published in Annals of Human Biology, 2023
Fuzuki Mizuno, Yasuhiro Taniguchi, Osamu Kondo, Michiko Hayashi, Kunihiko Kurosaki, Shintaroh Ueda
High-throughput sequencing technologies developed in recent decades have enabled us to acquire a large number of nucleotide and genome-wide sequences. In addition, their costs have decreased dramatically. As a result, ancient genome analysis is not restricted to well-preserved ancient human samples anymore but can be used for a wide range of ancient human samples. Since maternally inherited mitochondrial DNA/genome exhibits significant differences in nucleotide sequence among individuals, it has been used as a valuable index not only for individual identification of maternal relationships but also for genetic relationships among human populations. Here, we aimed to determine the entire nucleotide sequences of the mitochondrial genome (mitogenome) of an ancient human individual remains excavated from an 8200–8600 cal BP Initial Jomon archaeological site, the Iyai rock shelter site in Gunma Prefecture, central Honshu, Japan. We also investigated the matrilineal relationships among seven individuals. Although multiple haplogroup data were determined by PCR genotyping alone, we specifically compared the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.
Experimental and computational models to investigate intestinal drug permeability and metabolism
Published in Xenobiotica, 2023
Jinyuan Chen, Ziyun Yuan, Yifan Tu, Wanyu Hu, Cong Xie, Ling Ye
An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities (Bauer and Thiele 2018). Common approaches to investigating the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by construction data- or knowledge-driven networks that represent microbe interactions. For example, network-based approaches are used to identify relevant microbes or metabolites of the human gut microbiota (Faust et al. 2012). Moreover, constraint-based reconstruction and analysis (COBRA) are based on genome-scale metabolic reconstructions, which are formalised as metabolic models to simulate biologically relevant physiological states (Feist and Palsson 2008). These approaches drive further research on the human microbiota, mechanistically predicting different treatments for various diseases.