Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

Ilgisonis, Ekaterina V.; Vavilov, Nikita E.; Ponomarenko, Elena A.; Lisitsa, Andrey; Poverennaya, Ekaterina V.; Zgoda, Victor G.; Radko, Sergey P.; Archakov, Alexander I.

doi:10.3389/fgene.2021.674534

Cited by 9 publications

(13 citation statements)

References 26 publications

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“…We found that both Illumina and ONT showed good concordance between replicates, while the former platform performed better. This finding is in line with previous results [ 6 , 42 ]. The gene ranks correlation between both platforms was also relatively high, while there were genes whose expression was detected only by one of them.…”

Section: Discussionsupporting

confidence: 94%

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Pyatnitskiy

Arzumanian

Radko

et al. 2021

Biology

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Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed—ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments.

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Section: Discussionsupporting

confidence: 94%

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Pyatnitskiy

Arzumanian

Radko

et al. 2021

Biology

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“…It should also be taken into account that different sequencing platforms have advantages and disadvantages. Therefore, a combination of several of them may be needed for a comprehensive analysis of gene expression [125]. Besides, computational models [126], such as ML, have been applied to these studies [127], including dimension reduction methods [128].…”

Section: Functional Genomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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“…Several platforms recently became commercially available such as Helicos Bio Sensing, Pacific Biosciences, BGI Group Complete Genomics, and Oxford Nanopore Technology. Each platform has its own advantages and disadvantages (Blom 2021;Broseus et al 2020), Thus, a multifold compound of them may be required for a deep analysis of gene phraseology (Ilgisonis et al 2021). In addition, computational models like machine learning have been exerted to these analyses (Bobrovskikh et al 2021;Liu et al 2021).…”

Section: Third Generationmentioning

confidence: 99%