Ramification Amplification: A Novel Isothermal DNA Amplification Method

Zhang, David Y.; Brandwein, Margaret; Hsuih, T.; Li, Hong Bo

doi:10.1007/bf03262045

Cited by 14 publications

(4 citation statements)

References 12 publications

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“…Concurrently, a distinct category of WGA techniques embodies isothermal methodologies. Preeminently, Multiple Displacement Amplification (MDA) reigns as the paradigmatic approach, characterized by isothermal random priming and extension orchestrated by φ29 polymerase, distinguished by its robust catalytic activity, minimal error propensity, and strand displacement competence [60,63]. Owing to φ29 polymerase's elevated fidelity, these techniques manifest augmented genome coverage vis-à-vis initial PCR-based methods, accompanied by mitigated error rates.…”

Section: /14mentioning

confidence: 99%

Insights into the Precision Medicine of Pancreatic Cancer: Single-Cell Analysis

Jamshidi,

Chaleshi

et al. 2024

J Chronic Dis Manag

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The rising incidence of pancreatic cancer (PC) is a global challenge of paramount importance. Understanding the complex nature of this disease is crucial for addressing various issues within the field, including early recurrence, metastasis, and the formidable resistance to chemotherapy and radiotherapy. The complexity of PC arises from the diverse biological phenotypes present in tumor cells, creating a mosaic-like diversity. The lack of comprehensive insights into the functional aspects of cellular and molecular components further complicates treatment, leading to suboptimal outcomes. To tackle these intricacies, researchers must explore the cellular and molecular foundations of this multifaceted disease. Profiling cellular transcriptomes becomes a powerful tool for understanding the subtle heterogeneity in complex cellular populations within tissues. This approach allows for the deconstruction of molecular processes at the individual cell level, revolutionizing our understanding of cellular identity and function. By carefully examining differences in single-cell genomes, transcriptomes, and epigenetic profiles among tumor cells, both primary and metastatic, collected from patient samples, we gain insights into the diverse landscape of tumor heterogeneity. This perspective has significant implications for precision oncology in the context of pancreatic cancer. The current study provides a comprehensive assessment of the empirical basis for RNA sequencing technologies, the methodologies for single-cell isolation, and the conceptual framework for integrating these elements into prognostic assessment, genomic accessibility, transcriptional dynamics, and proteomic landscapes. By combining these components, the study aims to establish a coherent framework that facilitates the development of precision medicine approaches tailored to the unique challenges presented by pancreatic cancer.

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Section: /14mentioning

confidence: 99%

Insights into the Precision Medicine of Pancreatic Cancer: Single-Cell Analysis

Jamshidi,

Chaleshi

et al. 2024

J Chronic Dis Manag

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“…For single-cell isolation, various methods can be employed, each with different levels of accuracy, throughput, reproducibility, and usability. 74,75 Whole-genome amplification (WGA) approaches, such as degenerate oligonucleotide-primed PCR, 76,77 multiple displacement amplification, 78,79 multiple annealing and looping-based amplification cycles, and PicoPLEX, 80,81 can be utilized to amplify DNA before sequencing. Microfluidic devices have shown promise in reducing contamination during single-cell WGA, 82 and a novel two-step microfluidic droplet program has been proposed to realize efficient and large-scale parallel barcoding based on single-cell PCR.…”

Section: Single-cell Sequencing For Genomes (Scdna-seq)mentioning

confidence: 99%

Big data and single‐cell sequencing in acute myeloid leukemia research

Zou,

Zhang,

2023

MedComm – Oncology

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The advancement of diverse technologies has led to a substantial increase in valuable biomedical data, particularly in the field of acute myeloid leukemia (AML). Effective utilization of this wealth of data is crucial for attaining a comprehensive and in‐depth understanding of AML, thereby facilitating optimal diagnosis, treatment, and prognosis. Among the various approaches to data acquisition, single‐cell sequencing has emerged as an impressive tool. The developments of single‐cell sequencing methods have empowered researchers to analyze the genome, transcriptome, proteome, and epigenome data at the single‐cell level. It also offers a means to uncover fine information, providing unique prognostic insights and aiding in the identification of therapeutic targets. Furthermore, it enhances our understanding of AML heterogeneity, clonal evolution, and resistance mechanisms, ultimately leading to the development of better treatment strategies. In this review, we present an overview of AML as well as single‐cell sequencing technologies, then explore their potential contributions to AML research in different aspects, and provide some information about resources and data processing.

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“…Rolling circle amplification was first developed as a method in the mid-1990s ( 7 – 11 ). A typical application of rolling circle amplification is generating long, single-stranded DNA concatemers as the template for long-read sequencing as with Oxford Nanopore Technologies (ONT) platforms, allowing error correction by taking a consensus of the de-concatenated sequence ( 12 ).…”

Section: Introductionmentioning

confidence: 99%

Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis

et al. 2023

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Antimicrobial resistance is a global health threat, and drug resistant tuberculosis is a principal cause of antimicrobial resistance-related fatality. The long turnaround time and the need for high containment biological laboratories of phenotypic growth-based Mycobacterium tuberculosis drug susceptibility testing often commit patients to months of ineffective treatment, and there is a groundswell of effort in shifting from phenotypic to sequencing-based genotypic assays.

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Ramification Amplification: A Novel Isothermal DNA Amplification Method

Cited by 14 publications

References 12 publications

Insights into the Precision Medicine of Pancreatic Cancer: Single-Cell Analysis

Insights into the Precision Medicine of Pancreatic Cancer: Single-Cell Analysis

Big data and single‐cell sequencing in acute myeloid leukemia research

Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis

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