Library preparation for next generation sequencing: A review of automation strategies

Hess, Jacob Friedrich; Kohl, Thomas A.; Kotrová, Michaela; Rönsch, Kerstin; Paprotka, Tobias; Mohr, Vanessa; Hutzenlaub, Tobias; Brüggemann, Monika; Zengerle, Roland; Niemann, Stefan; Paust, Nils

doi:10.1016/j.biotechadv.2020.107537

Cited by 114 publications

(102 citation statements)

References 128 publications

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“…Understanding the genomic sequence of SARS-CoV-2 obtained from clinical specimens can help identify the COVID-19 pandemic origins, delineate transmission events, unravel clues to pathogenesis, and monitor viral evolution over time ( 404 – 408 ). Over the last few decades, DNA sequencing technologies have relied on modifications of Sanger sequencing, which was developed in the 1970s ( 409 ).…”

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

“…Over the last few decades, DNA sequencing technologies have relied on modifications of Sanger sequencing, which was developed in the 1970s ( 409 ). While Sanger sequencing technology is still used for small sequences (∼0.5 to 1 kb) such as single-gene targets, next-generation sequencing (NGS) technologies have allowed sequencing to be performed as massively paralleled reactions, allowing rapid access to complete genomes at a scale and cost that are feasible for many laboratories ( 404 – 406 , 410 – 412 ). For SARS-CoV-2 genomes of <30 kb, high-quality sequences can readily be obtained with NGS directly from clinical specimens using strategies like amplicon enrichment or bait capture techniques to favor the sequencing of the viral targets ( 413 ).…”

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

“…For SARS-CoV-2 genomes of <30 kb, high-quality sequences can readily be obtained with NGS directly from clinical specimens using strategies like amplicon enrichment or bait capture techniques to favor the sequencing of the viral targets ( 413 ). NGS involves technologies such as sequencing by synthesis, sequencing by ligation, and ion semiconductor sequencing (e.g., nanopore sequencing), each with its own advantages and limitations ( 404 – 406 , 410 – 412 ). The principle of each NGS technology has been reviewed elsewhere ( 404 – 408 ), and some of them are illustrated in Fig.…”

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

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Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

et al. 2021

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SUMMARY The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

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Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

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Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

et al. 2021

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“…Molecular phenotyping will thus become a crucial step in personalized medicine, and further exploration of pathophysiological diversity in diseases of the gut will greatly improve our ability to realize this personalized medicine. At the same time, single-cell techniques are evolving further, first of all, allowing for higher throughput and lower cost per sample ( 44 ). Other new developments in high-resolution transcriptome-wide technologies are capable to infer the spatial localization of the cells of which gene expression is measured, shedding more light on the functioning of the gut mucosa as an organ ( 45 , 46 ).…”

Section: Discussionmentioning

confidence: 99%

Understanding human gut diseases at single-cell resolution

Bigaeva

Venema

Weersma

et al. 2020

Human Molecular Genetics

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Our understanding of gut functioning and pathophysiology has grown considerably in the past decades, and advancing technologies enable us to deepen this understanding. Single-cell RNA sequencing (scRNA-seq) has opened a new realm of cellular diversity and transcriptional variation in the human gut at a high, single-cell resolution. ScRNA-seq has pushed the science of the digestive system forward by characterizing the function of distinct cell types within complex intestinal cellular environments, by illuminating the heterogeneity within specific cell populations and by identifying novel cell types in the human gut that could contribute to a variety of intestinal diseases. In this review, we highlight recent discoveries made with scRNA-seq that significantly advance our understanding of the human gut both in health and across the spectrum of gut diseases, including inflammatory bowel disease, colorectal carcinoma and celiac disease.

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“…Similar approaches are required to push increased utilization of sequencing to support the COVID-19 pandemic. For instance, the complexity and labor-intensive nature of sample and library preparation workflow could limit the widespread adoption of sequencing [165][166][167]. Efforts towards the automation and integration of sample and library preparation steps will enable increased adoption of sequencing platforms for COVID-19 pandemic management.…”

Section: Sample Preparationmentioning

confidence: 99%

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

et al. 2020

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The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.

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Library preparation for next generation sequencing: A review of automation strategies

Cited by 114 publications

References 128 publications

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

Understanding human gut diseases at single-cell resolution

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

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