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Genomic Informatics in the Healthcare System
Published in Salvatore Volpe, Health Informatics, 2022
Genomics is the systematic study on a whole-genome scale for the identification of genetic contributions to human conditions. Because NGS is a rapidly evolving technology and it has the ability to sequence the whole genome in a short period of time, it becomes possible to reveal all genetic information for medical purposes. Progress in our understanding of many fundamental biological phenomena has accelerated dramatically over the last decade driven by advances in genomic informatics. The advances in NGS genomic technologies have resulted in great achievements in genetic linkage, association studies, DNA copy number, and gene expression analysis. Furthermore, rapid advances in NGS have introduced inexpensive methods to acquire a large set of genetic data with potential applications across many specialties of medicine. Human genomic medicine is the use of broad-based genetic testing by patients and their healthcare providers to enhance routine clinical activities including diagnosis, risk assessment, tailored therapy, and more precise prognosis. Widespread marketing of genomic medicine services and health system implementations have increased the availability of testing to patients and their clinicians. In the future, the advances of NGS technologies can continue to contribute significantly to the personalized genomic medicine.
Genomic technologies
Published in Wendy A. Rogers, Jackie Leach Scully, Stacy M. Carter, Vikki A. Entwistle, Catherine Mills, The Routledge Handbook of Feminist Bioethics, 2022
One of the central goals in medical genomics is to understand the relationship between genotype (i.e. an individual’s collection of genes) and phenotype (i.e. an individual’s observable characteristics or traits). DNA sequencing, computation analysis and information technologies are essential tools for studying genomes and understanding these relationships. The power of these technologies has increased in outstanding ways in the last decade. The initial draft of the human genome took around 15 months to complete and cost around USD 300 million (Lander et al. 2001). The advent of next-generation sequencing (NGS) technologies now permits an unprecedented DNA sequencing throughput and speed at significant cost reduction (van Dijk et al. 2018). A draft of a human genome can now be produced in about one day for a few thousand US dollars. NGS technologies are able to perform sequencing of millions of small fragments of DNA in parallel (Levy and Boone 2019). NGS platforms can be used to sequence nearly all DNA of a given organism, i.e. whole genome sequencing (WGS), or the DNA parts that code for proteins, i.e. whole-exome sequencing (WES). These technologies can also sequence selected genes or fragments of a genome-related to a set of disorders, i.e. targeted sequencing. Using sophisticated computational algorithms, these DNA sequences are then reconstructed into the original genome or are mapped to a reference genome for analysis.
Understanding the Proteomics of Medicinal Plants under Environmental Pollution
Published in Azamal Husen, Environmental Pollution and Medicinal Plants, 2022
Pooja Singh, V.K. Mishra, Rohit Kashyap, Rahul Rawat
The novel ‘omics’ technologies enable researchers to identify the genetics underlying medicinal plant responses to adaptation mechanisms providing impetus to investigate the complex interplay between medicinal plants, their metabolism, secondary metabolite production, and the effect of polluting environment. The genome can be defined as the complete set of genes inside a cell. Genomics is, therefore, the study of the genetic make-up of organisms. Transcriptomics is the complete set of transcripts in a cell, and their abundance, for a specific developmental stage or physiological condition (Wang et al. 2009). Proteins play an important role in biological processes by providing structural support as well as physiological functions (Figure 12.1). The complete set of proteins in a cell refers to as proteome (Park 2004). Metabolomics is the latest technique, is defined as the quantitative complement of low-molecular-weight metabolites present in a cell under a given set of physiological conditions (Kell et al. 2005). In view of these, the changes at the cellular or subcellular level due to impacting influence of environmental stimulus can be more precisely understood through omics technologies (Figure 12.2).
New advances in the treatments of drug-resistant tuberculosis
Published in Expert Review of Anti-infective Therapy, 2023
Clustered Regularly-Interspaced Short Palindromic Repeats is an adaptive immune system of archaea and bacteria [42]. The role of CRISPR is as a component of the prokaryotic adaptive immune system. CRISPR has become a tool for genome editing. CRISPR-Cas systems cleave foreign DNA or RNA as part of the immune system [43]. Currently, there are two families and six subfamilies of the CRISPR-Cas system and several subtypes based on how they evolved. Class 2 and Class 1 systems have been used mostly for diagnostics. Class 1 could be used with class 2 or with the class 3 complex [44]. These system types are characterized by their acquisition, targeting, and action proteins [43]. By targeting the bacterial genome together with RNA, these endogenous CRISPR-Cas could be used as an antibacterial agent. This technique is only useful for bacteria with a functional CRISPR system [43]. M. tuberculosis has a CRISPR family of type III-A [61]
Emerging gene therapy products for RPGR-associated X-linked retinitis pigmentosa
Published in Expert Opinion on Emerging Drugs, 2022
Cristina Martinez-Fernandez de la Camara, Jasmina Cehajic-Kapetanovic, Robert E. MacLaren
Unlike cell therapy, gene therapy is a therapeutic strategy directed against the primary genetic defect. Depending on the mutated gene, the cellular function affected, and the type of the genetic mutation there are three main approaches: (1) gene replacement or augmentation strategy to target genetic mutations resulting in loss of protein function, for example in autosomal recessive disorders – the introduction of a healthy copy of the gene would provide the cell with the lost function; (2) gene silencing to disable the expression of a mutated gene that results in a gain of function, characteristic of autosomal dominant disorders; and (3) genome editing strategies aimed at correcting the altered genetic sequence directly. The field of genome editing, with new and improved techniques being developed constantly, has risen tremendously since it has the potential to treat most of the human diseases [23,24]. There are several gene therapy clinical trials ongoing to treat RP caused by mutations in different genes (Table 2).
A scoping review of longitudinal airway microbiota studies
Published in Expert Review of Respiratory Medicine, 2021
Tary Yin, Jae H. Jeong, Tim F. Hardcastle, Kristi Biswas, Richard G. Douglas
The pathogenic role of the microbiota (the micro-organisms of a particular site or habitat) in inflammatory diseases of the upper and lower respiratory tract remains unclear. Acute exacerbations in chronic diseases such as chronic obstructive pulmonary disease (COPD) and chronic rhinosinusitis often recur despite multiple courses of antimicrobial therapy [1–4]. In the majority of clinical practices, antibiotic prescribing is guided by culture results. However, culture-independent molecular techniques have shown that the microbiota is much more complex than culture results have suggested [3,5]. Molecular techniques such as next-generation sequencing target and amplify regions within the genomes of organisms. These sequences are matched to known sequences in databases to provide taxonomic identification. Sequencing the targeted region of the 16S rRNA (ribosomal ribonucleic acid) gene enables the identification of bacteria while other regions can be targeted to identify fungi (internal transcribed spacer 1, 18S, 23S) and viruses (5ʹ untranslated region, matrix, nucleocapsid) [6].