Genome sequencing guide: An introductory toolbox to whole‐genome analysis methods

Burian, Alexis; Zhao, Wufan; Lo, Te‐Wen; Thurtle-Schmidt, Deborah

doi:10.1002/bmb.21561

Cited by 13 publications

(4 citation statements)

References 47 publications

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“…After comparing the established sequences of obtained reads with sequences from genomic libraries (Microseq library (AB); Lab-specific custom library; Genbank BLAST (NCBI), and others), it is possible to determine the sequence and localization of nucleotides in the genome and reconstruct the entire genome sequence. This principle forms the basis of whole-genome sequencing [43].…”

Section: Resultsmentioning

confidence: 99%

Modern technologies for studying the genome of mycobacteria

Shapovalova,

Koshova,

Filimonova

2023

SR:MS

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Molecular technologies play a leading role in the laboratory diagnosis of tuberculosis and mycobacteriosis. The successes in studying the genome of Mycobacterium have contributed to significant progress in understanding the evolution, variability, and genetic diversity of pathogens, as well as the development of diagnostic technologies, including research into resistance to anti-tuberculosis drugs. The aim of this research is to conduct a comparative study of the spectrum of modern technologies for studying the genomes of mycobacteria and their impact on the efficiency of the laboratory diagnosis of tuberculosis. Materials and methods: a search for sources of information was carried out in the PubMed, Medline, Web of Science, and Google Scholar databases. Materials related to the technology of molecular diagnosis of tuberculosis and mycobacteriosis and for determining the susceptibility of pathogens to anti-tuberculosis drugs were selected. Results: it was determined that the modern methods for studying the genome of mycobacteria include amplification technologies (PCR analysis), hybridization, restriction, spoligotyping, sequencing, and their various combinations. The main methods are standard and modified protocols of PCR (RAPD-PCR, AP-PCR, rep-PCR, Real-time PCR, Inverse PCR, TB-LAMP, HIP, LM-PCR). Genomic Restriction Analysis can be used in studies of MTBC and NTM strains (RFLP, AFLP analysis, MIRU-VNTR genotyping). The most effective method for genome analysis is WGS. Complex methods that utilize a combination of molecular technologies allow for the direct detection of mycobacteria in clinical samples. Conclusions: the widespread application of genomic technologies in the study of mycobacteria will contribute to the effective implementation of the global WHO strategy for the prevention, treatment, and control of tuberculosis and mycobacteriosis

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Section: Resultsmentioning

confidence: 99%

Modern technologies for studying the genome of mycobacteria

Shapovalova,

Koshova,

Filimonova

2023

SR:MS

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“…Subsequently, an explosion of applications resulted in the creation of a new domain of biology, bioinformatics, with a slight change in the initial meaning of the word, now often restricted to genome‐based studies (Hogeweg, 2011). Yet, while this restriction is commonplace, the advent of genomics, with its related ‘omics’ studies (Yadav, 2007), has considerably expanded the domain, with only fuzzy boundaries with recently fashionable domains such as AI and image analysis (Burian et al ., 2021).…”

Section: Synthetic Biology In Silicomentioning

confidence: 99%

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Danchin

2021

Microbial Biotechnology

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Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computeraided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

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“…Schinzel–Giedion syndrome is a highly challenging disease with severe complications, including intellectual disability, malignant tumors, and congenital anomalies. Ultimately, using genetic sequencing [ 9 , 10 ], Schinzel–Giedion syndrome can be rapidly diagnosed, which significantly shortens the time required for treatment and significantly improves patient prognoses.…”

Section: Introductionmentioning

confidence: 99%

Identifying competing endogenous RNA regulatory networks and hub genes in alcoholic liver disease for early diagnosis and potential therapeutic target insights

Sun,

Lee,

Liu

et al. 2024

Aging

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Alcoholic liver disease (ALD) has a complex pathogenesis. Although early-stage ALD can be reversed by ceasing alcohol consumption, early symptoms are difficult to detect, and several factors contribute to making alcohol difficult to quit. Continued alcohol abuse worsens the condition, meaning it may gradually progress into alcoholic hepatitis and cirrhosis, ultimately, resulting in irreversible consequences. Therefore, effective treatments are urgently needed for early-stage ALD. Current research mainly focuses on preventing the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. However, challenges remain in identifying key therapeutic targets and understanding the molecular mechanisms that underlie the treatment of alcoholic hepatitis and cirrhosis, such as the limited discovery of effective therapeutic targets and treatments. Here, we downloaded ALD microarray data from Gene Expression Omnibus and used bioinformatics to compare and identify the hub genes involved in the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. We also predicted target miRNAs and long non-coding RNAs (lncRNAs) to elucidate the regulatory mechanisms (the mRNA-miRNA-lncRNA axis) underlying this progression, thereby building a competitive endogenous RNA (ceRNA) mechanism for lncRNA, miRNA, and mRNA. This study provides a theoretical basis for the early treatment of alcoholic hepatitis and cirrhosis and identifies potential therapeutic targets.

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Genome sequencing guide: An introductory toolbox to whole‐genome analysis methods

Cited by 13 publications

References 47 publications

Modern technologies for studying the genome of mycobacteria

Modern technologies for studying the genome of mycobacteria

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Identifying competing endogenous RNA regulatory networks and hub genes in alcoholic liver disease for early diagnosis and potential therapeutic target insights

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