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 11 publications

(3 citation statements)

References 47 publications

(94 reference statements)

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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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“…[4][5][6] Classic histopathological classification often ignores the heterogeneity of malignant tumors and cannot effectively guide the diagnosis and prognosis of patients. [7,8] Gliomas with the same pathological morphology are highly heterogeneous at the molecular level due to molecular genetic changes, resulting in very different tumor prognoses and responses to treatment. [9,10] Thus, genotype-based glioma typing can guide the individualized diagnosis and treatment of patients more objectively and reasonably.…”

Section: Introductionmentioning

confidence: 99%

Visual genetic typing of glioma using proximity‐anchored in situ spectral coding amplification

Chen

Deng

et al. 2023

Exploration

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Gliomas are histologically and genetically heterogeneous tumors. However, classical histopathological typing often ignores the high heterogeneity of tumors and thus cannot meet the requirements of precise pathological diagnosis. Here, proximity‐anchored in situ spectral coding amplification (ProxISCA) is proposed for multiplexed imaging of RNA mutations, enabling visual typing of brain gliomas with different pathological grades at the single‐cell and tissue levels. The ligation‐based padlock probe can discriminate one‐nucleotide variations, and the design of proximity primers enables the anchoring of amplicons on target RNA, thus improving localization accuracy. The DNA module‐based spectral coding strategy can dramatically improve the multiplexing capacity for imaging RNA mutations through one‐time labelling, with low cost and simple operation. One‐target‐one‐amplicon amplification confers ProxISCA the ability to quantify RNA mutation copy number with single‐molecule resolution. Based on this approach, it is found that gliomas with higher malignant grades express more genes with high correlation at the cellular and tissue levels and show greater cellular heterogeneity. ProxISCA provides a tool for glioma research and precise diagnosis, which can reveal the relationship between cellular heterogeneity and glioma occurrence or development and assist in pathological prognosis.

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

Cited by 11 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

Visual genetic typing of glioma using proximity‐anchored in situ spectral coding amplification

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