Novel omics technology driving translational research in precision oncology

Basu, Anubhav; Budhraja, Anshul; Juwayria,; Abhilash, Dasari; Gupta, Ishaan

doi:10.1016/bs.adgen.2021.08.003

Cited by 6 publications

(4 citation statements)

References 178 publications

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“…The library preparation protocols currently used for scRNA-seq are either plate-based, well-based, or droplet-based, depending on the cell separation method ( 15 ). Plate-based methods rely on physically isolating cells into 96- or 384-well plates and have low scalability.…”

Section: Advances In Single-cell Full-length Rna Capturementioning

confidence: 99%

Advances in single-cell long-read sequencing technologies

Gupta,

O’Neill,

Wolvetang

et al. 2024

NAR Genomics and Bioinformatics

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With an increase in accuracy and throughput of long-read sequencing technologies, they are rapidly being assimilated into the single-cell sequencing pipelines. For transcriptome sequencing, these techniques provide RNA isoform-level information in addition to the gene expression profiles. Long-read sequencing technologies not only help in uncovering complex patterns of cell-type specific splicing, but also offer unprecedented insights into the origin of cellular complexity and thus potentially new avenues for drug development. Additionally, single-cell long-read DNA sequencing enables high-quality assemblies, structural variant detection, haplotype phasing, resolving high-complexity regions, and characterization of epigenetic modifications. Given that significant progress has primarily occurred in single-cell RNA isoform sequencing (scRiso-seq), this review will delve into these advancements in depth and highlight the practical considerations and operational challenges, particularly pertaining to downstream analysis. We also aim to offer a concise introduction to complementary technologies for single-cell sequencing of the genome, epigenome and epitranscriptome. We conclude by identifying certain key areas of innovation that may drive these technologies further and foster more widespread application in biomedical science.

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Section: Advances In Single-cell Full-length Rna Capturementioning

confidence: 99%

Advances in single-cell long-read sequencing technologies

Gupta,

O’Neill,

Wolvetang

et al. 2024

NAR Genomics and Bioinformatics

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“…Since its discovery about 70 years ago in human plasma, it has been an area of research interest for clinical applications owing to its noninvasive nature [137]. Characteristics of cfDNA could vary in size, DNA methylation and repeating sequences [138]. These characteristics differ based on the type of disease, and hence may be useful in the detection of specific diseases.…”

Section: Vascular Endothelial Cell Specific Cell-free Dnamentioning

confidence: 99%

The Future of Kawasaki Disease Diagnosis: Liquid Biopsy May Hold the Key

Markandran,

Clemente,

Tan

et al. 2024

Preprint

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Kawasaki disease is a febrile illness characterised by systemic inflammation of small- and medium-sized blood vessels which commonly occurs in young children. Although self-limiting, there is a risk of developing coronary artery lesions as disease progresses with delay in diagnosis and treatment. Unfortunately, the diagnosis of KD continues to remain a clinical dilemma. Thus, this article not only summarises the key research gaps associated to KD, but also evaluates the possibility of using circulating endothelial injury biomarkers such as, circulating endothelial cells, endothelial microparticles and vascular endothelial cell-free DNA, as diagnostic and prognostic tool of KD: a “liquid biopsy” approach. The challenges of translating liquid biopsies to use in KD, and the opportunities for improvement in its diagnosis and management that such translation may provide are discussed. The use of endothelial damage markers, which are easily obtained via blood collection, as diagnostics is promising and we hope this will be translated to clinical applications in the near future.

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“…This has been made possible with the recently developed spatial transcriptomics sequencing (ST-Seq). ST-Seq provides the spatial information, i.e where the cells and gene expression signals come from in a tissue section and helps understand cellular interactions [1]. ST-Seq uses histological images where the tissue is sliced and fixated to a microscopic slide with oligos incorporated on the slide's surface.…”

Section: Visium Probesmentioning

confidence: 99%

Spurious off-target signals from potential lncRNAs by 10X Visium probes

Prakrithi

Sami

Jain

et al. 2022

Preprint

Self Cite

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Spatial transcriptomics has revolutionized molecular profiling of tissues in a spatial context, especially in the study of cancer heterogeneity. 10X Genomics facilitates spatial gene expression profiling platforms to help work with fresh-frozen (FF) and formalin fixed paraffin embedded (FFPE) tissues. FF analysis is based on polyA capture of RNAs while FFPE analysis uses a pre-designed set of probes to capture transcripts of coding genes. Previously, we used FFPE spatial data as a 'negative control' in a study to identify novel non-coding RNAs in FF data. Interestingly, we find and report that certain target probes used in FFPE show off-target signals from lncRNAs. The Space Ranger pipeline of 10X Visium counts the expression of these potential off-targets to be that of the corresponding target gene, some of which have known implications in cancer and its diagnosis. Therefore, relying on this technology is not ideal to investigate expression of the genes reported in this study. We hereby recommend excluding those genes in any downstream analysis of FFPE datasets and to design probes with better specificity, considering the sequence similarity between genes and non-coding RNAs.

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Novel omics technology driving translational research in precision oncology

Cited by 6 publications

References 178 publications

Advances in single-cell long-read sequencing technologies

Advances in single-cell long-read sequencing technologies

The Future of Kawasaki Disease Diagnosis: Liquid Biopsy May Hold the Key

Spurious off-target signals from potential lncRNAs by 10X Visium probes

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