Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization

Sager, Monica; Yeat, Nai Chien; Stadt, Stefan Pajaro-Van der; Lin, Chih-Lung; Ren, Qiuyin; Lin, Jimmy C.

doi:10.1586/14737159.2015.1105133

Cited by 36 publications

(20 citation statements)

References 94 publications

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“…These class-specific estimates of RNA abundance indicate that ∼90% of the human transcriptome by mass is composed of rRNA, while the highest number of molecules per cell (MPC) is attributed to tRNA (Waldron and Lacroute 1975;Wolf and Schlessinger 1977). Other methods such as reverse transcription quantitative PCR (RT-qPCR) (Ginzinger 2002;Shakeel et al 2017), digital PCR (dPCR) (Whale et al 2012;Hayden et al 2013;Witwer et al 2013;Morley 2014;Sager et al 2015), and in situ hybridization (e.g., FISH) (Vera et al 2016) are also being used for RNA quantification, but their use remains limited to a relatively low number of RNAs and they are rarely utilized for comparisons between different classes of RNA. More recently, transcriptome sequencing has become the most frequently used method for large scale profiling of the transcriptome (Casamassimi et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

Boivin

Deschamps-Francoeur

Couture

et al. 2018

RNA

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Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. tructuredonoding (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing.

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Section: Introductionmentioning

confidence: 99%

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

Boivin

Deschamps-Francoeur

Couture

et al. 2018

RNA

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“…Particular interest in oncology is focused on the field of transcriptomics for the identification and quantification of the RNA in cells, tissues, or biological fluids, representing a powerful tool for the assessment of specific biological activities [52]. In a single RNA-Seq experiment, it is possible to investigate, not only gene expression, but also alternative splicing [53], novel transcripts [54,55], allele specific expression [56], gene fusions [57], and genetic variations [58,59].…”

Section: Methodologiesmentioning

confidence: 99%

Radiogenomic Analysis of Oncological Data: A Technical Survey

Incoronato

Aiello

Infante

et al. 2017

IJMS

116

106

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In the last few years, biomedical research has been boosted by the technological development of analytical instrumentation generating a large volume of data. Such information has increased in complexity from basic (i.e., blood samples) to extensive sets encompassing many aspects of a subject phenotype, and now rapidly extending into genetic and, more recently, radiomic information. Radiogenomics integrates both aspects, investigating the relationship between imaging features and gene expression. From a methodological point of view, radiogenomics takes advantage of non-conventional data analysis techniques that reveal meaningful information for decision-support in cancer diagnosis and treatment. This survey is aimed to review the state-of-the-art techniques employed in radiomics and genomics with special focus on analysis methods based on molecular and multimodal probes. The impact of single and combined techniques will be discussed in light of their suitability in correlation and predictive studies of specific oncologic diseases.

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“…Whereas commercial systems are available to measure ET emission by plants in closed environments such as storage packages or boxes (Caprioli and Quercia, 2014;Tolentino et al, 2018), analysis of plant hormones in plant tissues requires cutting edge laboratory equipment (Novak et al, 2017) and highly skilled analysts. Polymerase chain reaction (PCR) is standard in detection of plant pathogens (Lau and Botella, 2017) and Reverse Transcriptase (RT) PCR is a frequently used tool in human medicine to detect the expression of critical genes, e.g., in cancer diagnosis (Sager et al, 2015). To my knowledge, up to date no RNA-based tools are available for routine determination of internal quality of plant products such as cuttings.…”

Section: Physiological Outputsmentioning

confidence: 99%

Overcoming Physiological Bottlenecks of Leaf Vitality and Root Development in Cuttings: A Systemic Perspective

Druege

2020

Front. Plant Sci.

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Each year, billions of ornamental young plants are produced worldwide from cuttings that are harvested from stock plants and planted to form adventitious roots. Depending on the plant genotype, the maturation of the cutting, and the particular environment, which is complex and often involves intermediate storage of cuttings under dark conditions and shipping between different climate regions, induced senescence or abscission of leaves and insufficient root development can impair the success of propagation and the quality of generated young plants. Recent findings on the molecular and physiological control of leaf vitality and adventitious root formation are integrated into a systemic perspective on improved physiologically-based control of cutting propagation. The homeostasis and signal transduction of the wound responsive plant hormones ethylene and jasmonic acid, of auxin, cytokinins and strigolactones, and the carbon-nitrogen source-sink balance in cuttings are considered as important processes that are both, highly responsive to environmental inputs and decisive for the development of cuttings. Important modules and bottlenecks of cutting function are identified. Critical environmental inputs at stock plant and cutting level are highlighted and physiological outputs that can be used as quality attributes to monitor the functional capacity of cuttings and as response parameters to optimize the cutting environment are discussed. Facing the great genetic diversity of ornamental crops, a physiologically targeted approach is proposed to define bottleneck-specific plant groups. Components from the field of machine learning may help to mathematically describe the complex environmental response of specific plant species.

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Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization

Cited by 36 publications

References 94 publications

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

Radiogenomic Analysis of Oncological Data: A Technical Survey

Overcoming Physiological Bottlenecks of Leaf Vitality and Root Development in Cuttings: A Systemic Perspective

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